AFNI HISTORY
all levels
The levels of importance go from 1 to 5, with meanings:
1 - users would not care
2 - of little importance, though some users might care
3 - fairly important
4 - a big change or new program
5 - IMPORTANT: we expect users to know
generated via the command : /var/www/html/pub/dist/bin/linux_gcc32/afni_history -reverse -html
---- log of AFNI updates (most recent first) ----
04 Nov 2009, RC Reynolds, Dimon, level 1 (MICRO), type 5 (MODIFY)
small change to check on sort problems
04 Nov 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
3dAllineate option for motion correction
volreg_method allows 3dAllineate, which is useful for DTI data.
Bug fix for post-transformation matrix and dataset view
03 Nov 2009, RW Cox, 3dREMLfit, level 1 (MICRO), type 0 (GENERAL)
Modify default -CORcut value from 0.0025 to 0.0011
To reduce likelihood of Choleski failure.
27 Oct 2009, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added support for optional LabelTable RGBA attributes
23 Oct 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -censor_fill and -censor_fill_par
These options are to zero-pad TRs that were censored by 3dDeconvolve.
21 Oct 2009, RW Cox, 1dAstrip, level 1 (MICRO), type 1 (NEW_PROG)
To remove Alpha characters from 1D-like files.
For my own ill-conceived plans for global domination. Cheap and not
perfect.
19 Oct 2009, RW Cox, 3dBlurInMask, level 1 (MICRO), type 2 (NEW_OPT)
add -preserve option, to keep Rick Reynolds from defecting to SPM
19 Oct 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options for using 3dBlurInMask, instead of 3dmerge
- added -blur_in_mask, -blur_in_automask and -blur_opts_BIM
- added -sep_char and -subj_curly
19 Oct 2009, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 2 (NEW_OPT)
New master options, dset1/2 terminology
New master_nnn_dxyz options to specify output resolution
dset1 and dset2 for non-EPI/anat alignment with lpa cost function
and turns off preprocessing steps
giant_move option turns off resampling and changes master options
Expanded help - including fuller description of edge method
Removed volume registration (motion correction) for anat2epi option
by default.
AFNI dataset views (+orig/+acpc/+tlrc) are maintained in output
depending on BASE, SOURCE or external dataset names for all output
16 Oct 2009, ZS Saad, afni, level 1 (MICRO), type 5 (MODIFY)
Turned off zeroing of uncommented text in .1D files
You can turn this behaviour back on by setting env
AFNI_1D_ZERO_TEXT to YES
16 Oct 2009, ZS Saad, 1dSEM, level 1 (MICRO), type 5 (MODIFY)
Setenv AFNI_1D_ZERO_TEXT to YES
16 Oct 2009, RW Cox, cs_qmed.c, level 1 (MICRO), type 0 (GENERAL)
added function to compute biweight midvariance
16 Oct 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -demean, to demean motion parameters, for example
The polort 0 values should be more accurate baseline constants.
Useful for creating a proper polort baseline w/3dSynthesize.
15 Oct 2009, ZS Saad, afni, level 1 (MICRO), type 5 (MODIFY)
Manual graph scaling forces AUTOSCALE [A] off
14 Oct 2009, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Direct viewing of pre-processed datasets in Dot xform
14 Oct 2009, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
New help window for Dot xform
14 Oct 2009, RC Reynolds, 3dTcat, level 1 (MICRO), type 5 (MODIFY)
allow creation of single volume dataset
as requested by N Vack (among many others)
13 Oct 2009, ZS Saad, quickspec, level 1 (MICRO), type 2 (NEW_OPT)
-tsnad to allow for setting anatomical flag and local domain parent
13 Oct 2009, ZS Saad, ConvertSurface, level 1 (MICRO), type 2 (NEW_OPT)
-xmat_1D allows for single row transform definition
08 Oct 2009, RW Cox, 3dPeriodogram, level 1 (MICRO), type 1 (NEW_PROG)
Does what it sound like, more or less, I hope.
07 Oct 2009, ZS Saad, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
1dplot's window frame now shows a title. See 1dplot -wintitle for details.
07 Oct 2009, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT)
Add -Mmask option to allow multiple mask values
For independent blurring (e.g., blur WM and GM separately).
07 Oct 2009, RW Cox, various, level 1 (MICRO), type 5 (MODIFY)
Modify srand48() init to use time()+getpid()
To make close-in-time runs have independent seeds.
06 Oct 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
More bug fixes related to ROI loading, and OSX's GLX problem
06 Oct 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -set_run_lengths option, for varying run lengths
Added for motion censoring and run padding.
02 Oct 2009, RW Cox, calc, level 1 (MICRO), type 5 (MODIFY)
Add mod(a,b) function to please RCR
02 Oct 2009, RW Cox, 1dgenARMA11, level 1 (MICRO), type 1 (NEW_PROG)
Generates ARMA(1,1) correlated noise time series
For simulation purposes.
02 Oct 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 5 (MODIFY)
also output cosines with -show_cormat_warnings
01 Oct 2009, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
9/29, defined isblank() in case of SOLARIS_OLD ... and then removed it
01 Oct 2009, RC Reynolds, @Reorder, level 1 (MICRO), type 5 (MODIFY)
minor changes:
- changed warnings on varying incidence counts (JB's woriding)
- discard indices which are not valid sub-bricks
- do not call 3dTstat if only one sub-brick
30 Sep 2009, RW Cox, 3dDeconvolve, level 1 (MICRO), type 5 (MODIFY)
Let user modulate amplitude of dmBLOCK
In particular, dmBLOCK(0) means the program modulates the amplitude
based on duration.
30 Sep 2009, RW Cox, 3dDeconvolve, level 1 (MICRO), type 5 (MODIFY)
Transpose row-wise 1D file on input when user screws up
1D files input to 3dDeconvolve are expected to have 1 column and many
rows. If the user gets this backwards, the program now transposes the
file internally, with an INFO message.
29 Sep 2009, RW Cox, afni, level 3 (MAJOR), type 5 (MODIFY)
InstaCalc is more-or-less ready
At least, I let Mike Beauchamp test it for his cunning plans.
29 Sep 2009, RW Cox, afni InstaCorr, level 1 (MICRO), type 0 (GENERAL)
Modify SeedBlur to SeedRad
Flat average over a sphere of given radius, instead of a Gaussian blur.
For Steve and Alex.
29 Sep 2009, RC Reynolds, @Reorder, level 2 (MINOR), type 1 (NEW_PROG)
script version of reorder plugin, for J. Bjork
29 Sep 2009, DR Glen, RetroTS, level 2 (MINOR), type 2 (NEW_OPT)
Flexible slice timing options
SliceOrder option allows for standard slice timing order
alt+z, alt-z, seq+z, seq-z, Custom and 1D text file input
29 Sep 2009, DR Glen, McRetroTS, level 2 (MINOR), type 2 (NEW_OPT)
Opt options available to compiled version
All options available through the Opt structure are now available
even with the compiled version of McRetroTS, making the compiled version
functionally equivalent to the RetroTS.m version
25 Sep 2009, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
InstaCalc is starting to work! Sort of. Crudely.
24 Sep 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed crashes on OS X 10.5 caused by OS X's buggy GLX implementation
24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Improved the 'star' blurring interface.
24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Setup final color blurring level.
24 Sep 2009, RW Cox, thd_1Ddset.c, level 1 (MICRO), type 0 (GENERAL)
Allow writing of 1D complex datasets instead of convert to float
For Larry Frank, who I love like a brother. Or a second cousin once
removed.
18 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Added option -n minnodes
18 Sep 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
Allow specifying external FreeSurfer color table.
17 Sep 2009, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Started writing InstaCalc
16 Sep 2009, RW Cox, parser,f, level 1 (MICRO), type 5 (MODIFY)
Add 'NOT' function as a synonym for 'ISZERO'
16 Sep 2009, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
FIx recursive calls to AFNI_set_viewpoint()
Caused by the UNCLUSTERIZE macro, which now checks to see if the
function redisplay is really needed.
16 Sep 2009, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Make the AFNI_FLASH_VIEWSWITCH variable default to NO, not YES
Sorry, Adam, but Ziad matters more to me than you do.
16 Sep 2009, RW Cox, All, level 1 (MICRO), type 0 (GENERAL)
Oh, and did I mention that Ziad Saad is Trouble?
Rasmus Birn isn't far behind, either.
16 Sep 2009, RC Reynolds, 3ddot, level 2 (MINOR), type 4 (BUG_FIX)
de-meaning data causes permission-based seg fault, apply means upon read
Found by Giuseppe Pagnoni.
16 Sep 2009, RC Reynolds, timing_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -scale_data for J Meltzer
16 Sep 2009, RC Reynolds, plug_vol2surf, level 1 (MICRO), type 2 (NEW_OPT)
can init debug level via AFNI_DEBUG_PLUG_VOL2SURF
14 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Allow specifying rmm in number of edges connecting nodes.
09 Sep 2009, ZS Saad, @fast_roi, level 2 (MINOR), type 2 (NEW_OPT)
Allow @fast_roi to accept existing TLRC transformed anatomy
09 Sep 2009, RW Cox, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
Add 'ball' options for mask generation
09 Sep 2009, RW Cox, 3dmaskave, level 1 (MICRO), type 2 (NEW_OPT)
Add box and ball options to this program, per Kyle Simmons
08 Sep 2009, RC Reynolds, realtime_receiver.py, level 1 (MICRO), type 5 (MODIFY)
bind to open host, so a /etc/hosts entry is not required
08 Sep 2009, DR Glen, whereami, level 2 (MINOR), type 5 (MODIFY)
Allows MNI_ANAT space for whereami
Subtracts 8mm I-S and uses MNI space transform to TTA
08 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Properly allows post-transformation matrix
04 Sep 2009, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
registration can now be consistent across runs
Reg Base can be 'Current': to set the base volume from the current run
(call this the old way), 'Current & Keep': use current run, but then
store that base and apply it to future runs, 'External Dataset': fix the
base from some chosen dataset.
Using 'Current & Keep' makes sense for realtime registration.
04 Sep 2009, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 2 (NEW_OPT)
if wget fails, try curl; added -curl and -testing options
03 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixes for certain combinations
Allowed BASE and SOURCE specification for oblique data
Allowed 3dWarpDrive volume registration with mean/max base
Removed anatomical output with oblique data and only epi2anat
02 Sep 2009, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Add ZeroToOne 1D transform function
28 Aug 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed make_CENSORTR_string, comma delimitation needs run: prefix
27 Aug 2009, RW Cox, AFNI image viewer, level 1 (MICRO), type 0 (GENERAL)
Keyboard Home key centers zoom window at crosshairs
Doesn't work if cropping and zooming are mixed. (The logistics are too
hard for my feeble brain.)
27 Aug 2009, RW Cox, AFNI image viewer, level 1 (MICRO), type 5 (MODIFY)
More crop region features
* Shift+Home centers crop region on the crosshairs
* Shift/Ctrl+arrow now respect image flip status
* Environment variable AFNI_IMAGE_CROPSTEP sets sign and size of crop
region shifting with Shift+arrow keys
* If this doesn't make John Butman happy, I don't know what will.
27 Aug 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed motion_ prefix in '3dDeconvolve -censor'
Found by B Bones.
27 Aug 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT)
added -regress_local_times, -regress_global_times
Since the -local_times and -global_times options in 3dDeconvolve must be
processed before the stimuli they refer to, it does nothing to pass them
via -regress_opts_3dD. Hence, the options are needed.
26 Aug 2009, RW Cox, 3dFFT, level 2 (MINOR), type 1 (NEW_PROG)
Compute spatial 3D FFT of a dataset
* This is for John Butman
* Was started a long time ago, but only finished today
* Probably useless
26 Aug 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
in scaling block, explicitly remove any negative data values
25 Aug 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Provide keystroke fine control over cropping in image viewer
Shift+arrowkey = scroll crop window
Ctrl+arrowkey = resize crop window
Right-click on crop button = menu to set size exactly
Hint on crop button = shows crop parameters
25 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
if volreg block, always create motion_${subj}_enorm.1D
25 Aug 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 5 (MODIFY)
with -censor_motion, also output PREFIX_enorm.1D
24 Aug 2009, RW Cox, mrilib.h, level 1 (MICRO), type 4 (BUG_FIX)
CABS macro fails if complex number has huge components
This is Larry Frank's fault, of course.
24 Aug 2009, RW Cox, 3dAFNItoNIML, level 1 (MICRO), type 2 (NEW_OPT)
Add -ascii option == way to dump dataset in plain text
21 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_censor_motion and -regress_censor_prev
Motivated by L Thomas and B Bones.
21 Aug 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -show_censor_count
20 Aug 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added motion censoring options
Added -censor_motion, -censor_prev_TR, -collapse_cols, -extreme_mask,
-set_tr, -write_censor and -write_CENSORTR.
Also modified afni_util.py, lib_afni1D.py and option_list.py.
14 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -align_epi_ext_dset, to align anat to external EPI
This may be important for multi-channel coil EPI data with low internal
structural contrast. Users might align to the first (pre-steady-state)
TR, even though that volume is not used in the analysis.
13 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -volreg_tlrc_adwarp, to apply a manual Talairach transformation
11 Aug 2009, RW Cox, cs_symeig.c, level 1 (MICRO), type 0 (GENERAL)
Speedup first_principal_vectors() -- for 3dmaskSVD and 3dLocalSVD
By hand tweaking the normal matrix calculation loops
11 Aug 2009, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
Make handedness warning more explicit
10 Aug 2009, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Fix crash reported by Ziad and Rick
In afni_setup_viewing(), fim_now might not be valid -- so allow for
that.
10 Aug 2009, RW Cox, 3dABoverlap, level 1 (MICRO), type 5 (MODIFY)
Modified to skip automask if dataset is byte-valued with 1 volume
10 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
truncate min dim to 3 sig bits for -volreg_tlrc_warp/-volreg_align_e2s
The old default was 2 bits, -volreg_warp_dxyz overrides.
10 Aug 2009, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 5 (MODIFY)
allow processing of -overwrite and AFNI_DECONFLICT
06 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed problems found by I Mukai and K Bahadur
- fixed -volreg_align_to base as applied in align_epi_anat.py
- fixed blur 'averages' computation when only one run
04 Aug 2009, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT)
added basic demo interface and itemized exception traps
31 Jul 2009, RC Reynolds, prompt_user, level 1 (MICRO), type 5 (MODIFY)
apply some escape sequences, mostly to display newlines
29 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed creation of extents mask when only 1 run
28 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 5 (MODIFY)
if known, require proper slice regressor ordering in -slibase* opts
27 Jul 2009, RW Cox, libmri, level 1 (MICRO), type 5 (MODIFY)
Add function mri_get_tempfilename() to mri_purger.c
To return a unique filename in a temp directory. Sort of like a fancy
version of the C library function tmpnam().
27 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
use -slibase_sm instead of -slibase in 3dREMLfit
27 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -slibase_sm, for slice-major ordering of regressors
RetroTS and afni_proc.py were incorrectly using this ordering.
** Analysis done prior to this probably needs to be re-done.
27 Jul 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_labels and -show_label_ordering
27 Jul 2009, RC Reynolds, plug_realtime, level 1 (MICRO), type 2 (NEW_OPT)
added Y/N AFNI_REALTIME_reset_output_index, to start each dset at 001
Also, changed prefix seperator to double underscore '__'.
27 Jul 2009, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
added SOLARIS_OLD atanhf #define to machdep.h
24 Jul 2009, RW Cox, afni.h, level 1 (MICRO), type 0 (GENERAL)
Replaced VERSION with AVERZHN to avoid conflicts with SVMlight
So AFNI doesn't have a VERSION any more, it has an AVERZHN.
24 Jul 2009, RW Cox, THD_open_3dcalc(), level 1 (MICRO), type 0 (GENERAL)
Modify to use globally unique filename every time, fer shur.
cf. code in file thd_mastery.c, using the UNIQ_idcode() function in
niml_uuid.c to create a unique filename
23 Jul 2009, RW Cox, 3dTfitter, level 1 (MICRO), type 2 (NEW_OPT)
Added -errsum option, to save error sums per voxel.
And a -help example showing how the error sum of squares can be used to
compute partial correlation coefficients of a fit.
23 Jul 2009, RW Cox, 3dLocalSVD, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug when all vectors are zero.
23 Jul 2009, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -partition option
23 Jul 2009, RC Reynolds, afni_run_R, level 2 (MINOR), type 5 (MODIFY)
allow any number of args, but where first is program, last is output
23 Jul 2009, DR Glen, MEMRI models, level 2 (MINOR), type 2 (NEW_OPT)
Single and Dual exponential models
New models for 3dNLfim that use single and dual exponential models
that are appropriate for MEMRI (Manganese Enhanced MRI
22 Jul 2009, RC Reynolds, realtime_reaceiver.py, level 3 (MAJOR), type 1 (NEW_PROG)
python replacement for serial helper
New 'data_choice' options can be added to compute_data_for_serial_port
for sending results of a different computation to the serial port.
21 Jul 2009, RW Cox, niml_feedme, level 2 (MINOR), type 1 (NEW_PROG)
Test and demo program showing how to set datasets to AFNI via NIML
An analog to rtfeedme. Sends volumes to AFNI using VOLUME_DATA
elements. Pretty rudimentary.
21 Jul 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Update widgets and viewing when VOLUME_DATA is added to a dataset
* Fix AFNI_setup_viewing() to update widgets properly when dataset nvals
changes
* Add function AFNI_update_dataset_viewing() to deal with viewing
changes that might be needed if a dataset is altered
17 Jul 2009, RW Cox, 3dLocalstat, level 1 (MICRO), type 5 (MODIFY)
speedup for OpenMP
Modify mri_nstats.c to use pre-malloc-ed workspaces, instead of a new
one for each calculation, which makes a big difference in OpenMP.
16 Jul 2009, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added option to force autoscale on the graphing window
The option is accessible by pressing 'A' in the graph window
or under 'Graph->Opt->Scale->AUTO'.
16 Jul 2009, RW Cox, 3dmaskSVD, level 1 (MICRO), type 5 (MODIFY)
Speedup (a lot for large masks) by using new SVD routine.
16 Jul 2009, RC Reynolds, realtime_receiver.py, level 3 (MAJOR), type 1 (NEW_PROG)
replacement for serial_helper
16 Jul 2009, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY)
check for 'wget' and whine to user if missing
15 Jul 2009, RW Cox, 3dLocalSVD, level 1 (MICRO), type 0 (GENERAL)
Modify to use more efficient SVD routine
14 Jul 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -max_rest, to limit the maximum duration of rest periods
14 Jul 2009, DR Glen, afni, level 2 (MINOR), type 3 (NEW_ENV)
Added AFNI_ONE_OBLIQUE_WARNING
AFNI_ONE_OBLIQUE_WARNING = YES makes interactive spit out ONE warning
about obliquity per session then go quiet.
13 Jul 2009, RW Cox, 3dLocalstat, level 2 (MINOR), type 5 (MODIFY)
OpenMP
Also added option '-use_nonmask' to allow statistics to be computed for
voxels not in the mask (but presumably whose neighbors are in the mask).
07 Jul 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
warn users to modify script for _AM1 in case of basis function dmBLOCK
01 Jul 2009, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Modify AFNI_START_SMALL to pick smallest dataset of all.
Rather than the smallest 'anat' and smallest 'func', separately.
30 Jun 2009, RW Cox, various 3D programs, level 1 (MICRO), type 4 (BUG_FIX)
Remove keywords propagation stuff
e.g., 3dTcat and 3dbucket
Also, fix keywords printout buffer overflow in thd_info.c
29 Jun 2009, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
Fix memcpy bug in data extraction when using OpenMP. Ugghh.
26 Jun 2009, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Add 1D index jumping to "Jump to (ijk)"
26 Jun 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
comment changes and mod to afni_util.py for line wrapping
25 Jun 2009, RW Cox, 3dREMLfit, level 1 (MICRO), type 5 (MODIFY)
More tweaks to the OpenMP-ization. Only slightly better.
25 Jun 2009, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
fixed dz sent to RT plugin for oblique datasets
25 Jun 2009, RC Reynolds, 3dretroicor, level 1 (MICRO), type 4 (BUG_FIX)
pass MRI_IMAGE structs without const
24 Jun 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 0 (GENERAL)
Modify to use OpenMP more effectively.
Have to avoid use of Doug's matrix.c functions in the main loops, since
they do so much malloc/free, which blocks other threads from running.
Instead, rewrote versions of the needed functions that use pre-allocated
workspace arrays. Speedup is very good now for the REML setup and REML
voxel loops. Haven't decided whether to OpenMP-ize the GLSQ or OLSQ
loops, since these usually take much less time.
24 Jun 2009, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
applied print changes from B Feige (26 files):
3dfim.c afni.c afni_niml.c mri_free.c mrilib.h 3dmatmult.c NLfit_model.c
suma_datasets.h gifti/gifti_tool.c rickr/serial_helper.c
SUMA/ SUMA_3dSurfMask.c SUMA_ConvertSurface.c SUMA_CreateIcosahedron.c
SUMA_Load_Surface_Object.c SUMA_MapIcosahedron.c SUMA_NikoMap.c
SUMA_ParseCommands.h SUMA_SphericalMapping.c
SUMA_Surf2VolCoord_demo.c SUMA_Surface_IO.c SUMA_SurfWarp.c
SUMA_compare_surfaces.c SUMA_xColBar.c
svm/3dsvm.c svm/3dsvm_common.c volpack/vp_octree.c
23 Jun 2009, RW Cox, 3dTcorrMap, level 1 (MICRO), type 2 (NEW_OPT)
Add -Pmean option, based on poster I saw at HBM.
23 Jun 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX)
added 4 checks of alloc() returns
17 Jun 2009, RW Cox, 3dREMLfit, level 1 (MICRO), type 0 (GENERAL)
OpenMP-ization
Some speedup, but need to work on not doing malloc/free so much in the
REML_func function!
17 Jun 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
version 2.0 : call e2a alignment and warp to standard space ready
- mask warped EPI by its extents (at volreg step)
- added -volreg_no_extent_mask, to block this masking
- added 'extents' to list of mask in -mask_apply
- change block dividers to more visual '===' with block names
17 Jun 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -make_3dd_contrasts and used general accuracy in block durations
17 Jun 2009, DR Glen, RetroTS.m, level 2 (MINOR), type 4 (BUG_FIX)
Number of TRs found incorrectly because of rounding
17 Jun 2009, DR Glen, McRetroTS.m, level 2 (MINOR), type 1 (NEW_PROG)
Matlab Compilable version of RetroTS.m
This version calls the RetroTS function, but can be compiled
for users that either do not have Matlab, a required toolbox
or want to use this function in a shell script more easily.
16 Jun 2009, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
Add '-ytran' option
Apply an expression to the time series, to transform it prior to
plotting. To elide the use of 1deval.
15 Jun 2009, RW Cox, AlphaSim, level 1 (MICRO), type 4 (BUG_FIX)
OpenMP: cdfnor() and other functions are not thread-safe
Make use of cdfnor() 'critical'. Longer term: should patch the nifti
CDF functions to avoid static variables where possible.
15 Jun 2009, RC Reynolds, 3dmerge, level 2 (MINOR), type 5 (MODIFY)
allowed short/byte datasets to use FIR blur, so no Fourier interpolation
Also added Y/N AFNI_BLUR_INTS_AS_OLD env var to use previous method.
15 Jun 2009, DR Glen, BrikLoad.m, level 2 (MINOR), type 4 (BUG_FIX)
Typo in BrikLoad
Gremlin got to Pixy
12 Jun 2009, RC Reynolds, xmat_tool.py, level 1 (MICRO), type 5 (MODIFY)
used some wx IDs, per Daniel's suggestion
11 Jun 2009, RW Cox, AlphaSim, level 2 (MINOR), type 5 (MODIFY)
Added computation of analytic approximation of Alpha(i) for large i
Uses a modified extreme value distribution, which looks pretty good.
11 Jun 2009, RW Cox, zgaussian, level 1 (MICRO), type 4 (BUG_FIX)
'long' should be 'int' on 64 bit systems, when doing bit twiddling
11 Jun 2009, RW Cox, parser, level 1 (MICRO), type 5 (MODIFY)
Added posval() function, and treat '[]' as '()' for clarity.
11 Jun 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added masking abilities
- in mask block, try to create anat and group masks
- added -mask_apply option, for choosing mask to apply to regression
- added -align_opts_aea, for extra opts to align_epi_anat.py
09 Jun 2009, RW Cox, AlphaSim, level 1 (MICRO), type 0 (GENERAL)
Modify to use OpenMP (parallelize across iterations)
08 Jun 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
added -despike_mask, fixed missing block warning, reordered terminal opts
08 Jun 2009, RC Reynolds, afni_base.py, level 1 (MICRO), type 5 (MODIFY)
added many afni_name descripts to __doc__ lines, check error in dset_dims
03 Jun 2009, RW Cox, bbox.c, level 1 (MICRO), type 5 (MODIFY)
Modify string list chooser to do Browse select callback via arrows
To make consistent the ways of browsing thru the dataset choosers in
AFNI.
03 Jun 2009, RC Reynolds, 3dcopy, level 1 (MICRO), type 5 (MODIFY)
changed 'missing dataset' ERROR to 'missing view dataset' WARNING
01 Jun 2009, RW Cox, debugtrace.h, level 1 (MICRO), type 5 (MODIFY)
Add ability to suspend/restore function traceback stack
Disable stack when OpenMP parallel section is engaged.
29 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -execute and now fail if block options have no corresponding blocks
29 May 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
improved line wrapping
29 May 2009, RC Reynolds, @build_afni_Xlib, level 1 (MICRO), type 5 (MODIFY)
added -m64 if building for lib64 on a mac, fixed CFLAGS to allow a list
28 May 2009, RC Reynolds, strblast, level 2 (MINOR), type 4 (BUG_FIX)
partial words had resulted in skipping ahead
found by R Notestine of UCSD
28 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
example updates for AFNI_data4 and new options
27 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
updates for alignment/warp/varying run lengths
- added -volreg_warp_dxyz option
- if align a2e, add -no_ss to @auto_tlrc
- for varying run lengths, fixed application of '-volreg_align_to last'
and the -regress_est_blur_* options
(blur estimation loops were modified for this)
- warping to new grid truncates to 2 significant bits (if < 2 mm)
26 May 2009, RW Cox, thd_1Ddset.c, level 1 (MICRO), type 5 (MODIFY)
Change way names are used in output of .1D 'datasets'
(a) If prefix starts with '-' or 'stdout', write results to stdout as a
'pure' 1D formatted file (no NIML header),
(b) Otherwise, if -prefix option had a directory name attached, use that
instead of always using the current working directory.
22 May 2009, ZS Saad, @FS_roi_label, level 2 (MINOR), type 1 (NEW_PROG)
A script to get FreeSurfer parcellation and annotation labels
The script is used to return a label associated with a FreeSurfer
annotation or parcellation integer label.
22 May 2009, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Check if im3d->fim_now is NULL in AFNI_func_overlay()
21 May 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Additional check for caret-version string
It seems that the syntax for caret-version has changed
slightly and was being missed by SUMA. As a result, Caret
surfaces were not being properly aligned with the volumes.
21 May 2009, ZS Saad, imcat, level 1 (MICRO), type 2 (NEW_OPT)
Now output a grayscale 1D version of an image
That is done by adding a .1D to the -prefix parameter.
21 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added 'align' processing block and -volreg_align_e2a option
20 May 2009, RW Cox, realtime plugin, level 2 (MINOR), type 5 (MODIFY)
Modified to allow realtime 3D registration on complex inputs
Mostly a change in mri_3dalign.c, to take the movement estimation done
on the magnitude image and apply it to the 2 component images.
20 May 2009, RW Cox, realtime plugin, level 1 (MICRO), type 3 (NEW_ENV)
Also modify it to limit the number of open controllers.
cf. AFNI_REALTIME_MAX_CONTROLLERS
20 May 2009, G Chen, 3dMEMA.R, level 4 (SUPER), type 1 (NEW_PROG)
Mixed-Effects Meta Analysis (MEMA)
This is an R program that runs group analysis in a truly random/
mixed-effects sense by taking both beta and t-statistic as input
instead of beta value only in the conventional method. See more
details at http://afni.nimh.nih.gov/sscc/gangc/MEMA.html
19 May 2009, ZS Saad, @ROI_Corr_Mat, level 3 (MAJOR), type 1 (NEW_PROG)
A script to calculate correlation matrices between ROI time series
Calculates the correlation matrices between average time series from ROIs
defined in a mask volume. Script was written with Hang Joon Jo.
19 May 2009, ZS Saad, prompt_user, level 2 (MINOR), type 1 (NEW_PROG)
Prompts user for input with an X window
19 May 2009, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
Added -zerofill and -roisel options
Added options to force output for empty ROIs.
19 May 2009, ZS Saad, 1ddot, level 2 (MINOR), type 2 (NEW_OPT)
Added -okzero to keep program from exiting with all zero input
Added options to force output for empty ROIs.
19 May 2009, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT)
Modified time out for DriveSuma to 5 minutes
Time out can be controlled by environment variable SUMA_DriveSumaMaxWait
19 May 2009, RC Reynolds, 3dbucket, level 1 (MICRO), type 5 (MODIFY)
suggest -overwrite if -glueto is not allowed (for Mike B)
18 May 2009, RW Cox, 3dDespike, level 1 (MICRO), type 0 (GENERAL)
Speedup by OpenMP
Also required changes to mcw_malloc.c to mark various sections as
'critical' and to cl1.c to remove 'static' from all variables generated
from Fortran.
15 May 2009, RW Cox, afni InstaCorr, level 2 (MINOR), type 0 (GENERAL)
Remove OpenMP; carry out setref on all locked controllers
15 May 2009, RW Cox, afni InstaCorr, level 1 (MICRO), type 0 (GENERAL)
SeedBlur + locked InstaCorr-ology
15 May 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
added -volreg_tlrc_warp option: can warp to standard space at volreg step
15 May 2009, RC Reynolds, afni_util, level 1 (MICRO), type 2 (NEW_OPT)
added get_truncated_grid_dim
14 May 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
no 'rm rm.*' if such files were not created
14 May 2009, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
fixed -glt_label > -num_glt error message and -dmbase def for polort >= 0
13 May 2009, RW Cox, InstaCorr+3dBlurInMask, level 2 (MINOR), type 0 (GENERAL)
Added OpenMP support for blurring to these programs
Parallelization occurs across sub-bricks -- speedup is significant.
12 May 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed 'cat' of 'across-runs' ricor regressors
11 May 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
InstaCorr changes
* Save seed time series into the 1D timeseries library for graphicking
* Modify progress printouts slightly
08 May 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Better display of ROI contours on patches
Suma now correctly handles ROI display when the ROIs
contain nodes that are not in the patch. Also, on flat surfaces,
ROI contours are drawn raised so that they float over flat surfaces.
08 May 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
The script now automatically turns FS annot files to SUMA ROI files
08 May 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Instacorr updates
* Can Write A_ICOR datasets using new allow_directwrite variable
* Disable InstaCorr when switching sessions and views
* Notify renderer (DRAWNOTICE) when changes made
* Shift-Ctrl-Left-Click does crosshair shift + InstaCorr Set
08 May 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
tlrc (for anat) is now a processing block, for easy manipulation
08 May 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
small cut-n-paste errors in db_mod.py and afni_util.py
07 May 2009, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
FIxes/upgrades for InstaCorr
* memory problem fixed by malloc-ing sizeof(float *)
-- not sizeof(float) -- for a float ** variable!
* add dataset labels
* add statistical parameters (including FDR)
* add help
06 May 2009, RW Cox, afni, level 3 (MAJOR), type 2 (NEW_OPT)
First edition of InstaCorr!
Rough around the edges, but gnarly-ific to the level of the first
inaccessible cardinal!
05 May 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 4 (BUG_FIX)
Added 'd' and 'j' keys
05 May 2009, ZS Saad, 3dRank, level 2 (MINOR), type 1 (NEW_PROG)
A program that substitutes a voxel's value by that value's rank
05 May 2009, RC Reynolds, plug_render, level 2 (MINOR), type 5 (MODIFY)
now built from plug_null.c, so it will no longer be available
05 May 2009, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 1 (NEW_PROG)
another script to update the AFNI package
01 May 2009, RW Cox, 3dBlurInMask, level 2 (MINOR), type 1 (NEW_PROG)
Like 3dBlurToFWHM, but simpler.
01 May 2009, RW Cox, thd_bandpass.c, level 1 (MICRO), type 4 (BUG_FIX)
modified to make it actually work, including lowpass and highpass
01 May 2009, RC Reynolds, Makefile.linux_xorg7_64, level 1 (MICRO), type 5 (MODIFY)
link to local libGLws.a, as with 32-bit xorg7 package
01 May 2009, DR Glen, 1dSEM, level 2 (MINOR), type 4 (BUG_FIX)
Tree growth fix
Fixed bug in tree growth and improved output text
30 Apr 2009, RW Cox, 1dBandpass, level 1 (MICRO), type 1 (NEW_PROG)
for .. Bandpassing!
Really just to test the new bandpassing functions for inclusion into
AFNI's InstaCorr feature.
30 Apr 2009, RC Reynolds, vol2surf, level 2 (MINOR), type 2 (NEW_OPT)
return a node v2s time series when afni changes xhair position
30 Apr 2009, RC Reynolds, thd_niftiread, level 2 (MINOR), type 5 (MODIFY)
be sure to warn users when nifti is converted to float (w/dglen)
30 Apr 2009, RC Reynolds, 3dcalc, level 2 (MINOR), type 5 (MODIFY)
changed atan2(y,x) to proceed if y OR x is non-zero
29 Apr 2009, ZS Saad, SurfSmooth, level 2 (MINOR), type 4 (BUG_FIX)
-detprefix_* options now do something!
29 Apr 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT)
-nodelist* options to output node sequence forming ROI
29 Apr 2009, ZS Saad, MapIcosahedron, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash when using -it option for geometry smoothing
29 Apr 2009, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT)
-node_select_1D now respects node ordering
29 Apr 2009, ZS Saad, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT)
-VarThresh* options for obtaining counts at different thresholds
29 Apr 2009, RW Cox, afni, level 2 (MINOR), type 3 (NEW_ENV)
Make 'Where am I?' font size user controllable.
via AFNI_TTATLAS_FONTSIZE environment variable (editable).
29 Apr 2009, RW Cox, 3dTcorrMap, level 1 (MICRO), type 0 (GENERAL)
Add OpenMP support
29 Apr 2009, RW Cox, 3dTcorrMap, level 1 (MICRO), type 0 (GENERAL)
unroll innermost loop -- makes little difference :-(
29 Apr 2009, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
when opening -geomparent, allow for known non-afni extensions
29 Apr 2009, RC Reynolds, vol2surf, level 1 (MICRO), type 5 (MODIFY)
prep to return node v2s time series to suma, just check-in for now
modified: afni.h, afni_niml.c, afni_vol2surf.c, vol2surf.c, vol2surf.h
28 Apr 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Add duration argument to SPMGx basis functions for deconvolution.
For Tracy Doty, apparently.
28 Apr 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 5 (MODIFY)
uppercase file extensions are now valid
27 Apr 2009, RC Reynolds, 3dresample, level 1 (MICRO), type 5 (MODIFY)
show help if no arguments
23 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
updates to help and tcsh options
- added -f as a recommended tcsh option
- added help section 'SCRIPT EXECUTION NOTE'
- reordered help: intro, BLOCKS, DEFAULTS, EXAMPLES, NOTEs, OPTIONS
- shifted execution command to separate line
23 Apr 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
moved function comments into the functions as docstrings
23 Apr 2009, RC Reynolds, 3dresample, level 1 (MICRO), type 5 (MODIFY)
small changes to help
22 Apr 2009, DR Glen, @AddEdge, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Oblique edge display
Fixed bug with oblique data in edge display
20 Apr 2009, DR Glen, 3dAllineate, misc, level 1 (MICRO), type 5 (MODIFY)
1D file handling
Handle row and column selectors for 1D files better for most
AFNI programs. Returns error if improper row or column selection
17 Apr 2009, RC Reynolds, GIFTI, level 1 (MICRO), type 5 (MODIFY)
more -set_extern_filelist help, allow DA size to vary over external files
16 Apr 2009, RW Cox, All, level 2 (MINOR), type 4 (BUG_FIX)
Inadvertent recursion in afni_environ.c now blocked.
15 Apr 2009, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
Add -thick option
Plus: modify plot_ts.c to thicken the lines used for plotting the labels
(so the fancy characters are filled in a little).
14 Apr 2009, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
niml ROI files with empty ROI no longer crash suma/ROI2dataset
14 Apr 2009, RC Reynolds, NIfTI, level 2 (MINOR), type 2 (NEW_OPT)
added sample nifticlib program: clib_01_read_write.c
14 Apr 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 4 (BUG_FIX)
possible to have truncation cause a negative variance in stdev_ub
13 Apr 2009, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
fixed bug in printing censor message for -addbase and -slibase
11 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -volreg_regress_per_run
This is to apply the motion parameters of each run as separate regressors.
11 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -derivative and -set_nruns, fixed -show_cormat_warnings typo
11 Apr 2009, RC Reynolds, option_list.py, level 1 (MICRO), type 2 (NEW_OPT)
enhanced special option processing
- added check_special_opts(), to be called before any processing
- renamed -verbose_opts to -optlist_verbose
- added -optlist_no_show_count
11 Apr 2009, RC Reynolds, eg_main_chrono.py, level 1 (MICRO), type 5 (MODIFY)
removed -verbose opts (see -optlist_ options)
11 Apr 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed use of -regress_errts_prefix with blur est
11 Apr 2009, RC Reynolds, afni-general, level 1 (MICRO), type 2 (NEW_OPT)
added calls to opts.check_special_opts() in 7 more python programs:
gen_epi_review.py, make_random_timing.py, make_stim_times.py
neuro_deconvolve.py, python_module_test.py, timing_tool.py, ui_xmat.py
10 Apr 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Error in processing -slibase file with censoring
Typo in replacing input image with censored image caused the end of the
world (SEGV crash).
10 Apr 2009, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT)
added -use_last_elem option for setting DICOM elements
Can also use AFNI_DICOM_USE_LAST_ELEMENT environment variable.
10 Apr 2009, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -use_last_elem option for setting DICOM elements
10 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY)
fix for old versions of python, like on solaris
Each of copy.deepcopy(), sum(), and sort(reverse=True) failed.
09 Apr 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
'official' release with RETROICOR processing block: ricor
o added 'across-runs' ricor_regress_method
o added ricor information and usage to help (see 'RETROICOR NOTE')
o maintain unscaled shorts if they are input
o added -ricor_datum
09 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_cormat_warnings and -cormat_cutoff
08 Apr 2009, RW Cox, thd_filestuff.c, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_ALLOW_ARBITRARY_FILENAMES
Set this environment variable to YES to allow 'strange' characters into
AFNI created filenames. You should know what you are doing if you use
this variable!
08 Apr 2009, RW Cox, AFNI image viewer, level 2 (MINOR), type 5 (MODIFY)
Set MPEG 'pattern' for frames to reflect the Anim_dup setting.
This small change will make MPEG-1 (.mpg) files that are slowed down by
setting Anim_dup > 1 not significantly larger than full speed files, by
setting the frame pattern to 'IPPPP' where the number of Ps is the
number of duplicate frames (Anim_dup-1).
08 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_rows_cols option
06 Apr 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added support for '.', ',', and space keys, and 'shw_0'
06 Apr 2009, RW Cox, 3dmaskSVD, level 1 (MICRO), type 2 (NEW_OPT)
Modify to allow output of more than 1 singular vector.
Also, make the help more helpful.
06 Apr 2009, RW Cox, 3dLocalSVD, level 1 (MICRO), type 2 (NEW_OPT)
Add -vproj option
To project central voxel onto low-dimensional local SVD space.
04 Apr 2009, RW Cox, 3dmaskSVD, level 2 (MINOR), type 1 (NEW_PROG)
Like 3dmaskave, but does SVD principal vector instead of average
02 Apr 2009, RW Cox, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT)
Add -Thresh option
To save a count of how many other voxels are above threshold correlated
with each seed voxel.
02 Apr 2009, RW Cox, 3dLocalSVD, level 1 (MICRO), type 4 (BUG_FIX)
Fixed a little bug in 3dLocalSVD.
02 Apr 2009, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
changed CHECK_NIFTI to CHECK_NEEDS_FLOATS, including other dset types
02 Apr 2009, DR Glen, align_epi_anat.py, level 1 (MICRO), type 5 (MODIFY)
help update
Incorporated Bob's recommendations into help to make
various options clearer
01 Apr 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Arrow keys based navigation along surface.
See 'Alt+U-D' section in SUMA's interactive usage help.
01 Apr 2009, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
Added SUMA_KeyNodeJump variable
This variable controls number of nodes to jump with arrow keys navigation.
See suma -environment for complete list and defaults.
01 Apr 2009, RW Cox, realtime plugin, level 1 (MICRO), type 0 (GENERAL)
Enhanced a few error messages.
I wish people would READ the damn things, instead of calling me to
complain.
01 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
added 'ricor' processing block, for RETROICOR regressor removal
01 Apr 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
slight change in add_line_wrapper()
31 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Handling of double precision datatypes.
31 Mar 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added 'on the fly' dot product computation
This feature is only available with SUMA's -dev
option. It is still in testing mode and its
interface may change. If intrigued, see 'D' key's
help in SUMA's interactive usage help.
31 Mar 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added support for '[' and ']' keys and -view_surf
31 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
small changes, and prep for retroicor
- by default, the script will now terminate on any error
- added -exit_on_error, -check_setup_errors
- whine about block order problems
31 Mar 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -pad_to_many_runs, -reverse
31 Mar 2009, RC Reynolds, option_list.py, level 1 (MICRO), type 2 (NEW_OPT)
added global -verbose_opts option
31 Mar 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
added get_typed_dset_attr_list, enhanced decode_1D_ints
30 Mar 2009, RW Cox, 3dABoverlap, level 2 (MINOR), type 1 (NEW_PROG)
Computes various overlap and non-overlap statistics for 2 datasets.
Will resample dataset #B to match dataset #A, if needed. This program
is intended to check if two datasets are grossly not aligned, and has
little other purpose.
27 Mar 2009, RW Cox, FDR calculations, level 2 (MINOR), type 5 (MODIFY)
Changes/additions to mask operations for FDR curves.
3dREMLfit and 3dDeconvolve now generate an automask for the FDR curving
purposes, if no other mask is used. 3drefit has a new -FDRmask option
for computing the FDR curves correctly if no mask was used before.
26 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Support for reading/writing MNI .obj surfaces
26 Mar 2009, RW Cox, FDR, level 1 (MICRO), type 5 (MODIFY)
Change the way m1 is estimated for MDF 'hint'.
26 Mar 2009, RC Reynolds, option_list.py, level 1 (MICRO), type 5 (MODIFY)
base 'name' size on max len in show()
26 Mar 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
added helpstr to options
26 Mar 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
small array fix for older python in write()
25 Mar 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add -nobout option, to suppress baseline betas from -Rbeta/-Obeta.
Per the request of Michael S Beauchamp, University of Texas.
25 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
+view now comes from data: so it works with +tlrc
24 Mar 2009, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL)
Added -stim_times_subtract option
To allow adjustment of stimulus times due to removal of some images at
the start of each run.
ALSO: added -stim_time_millisec option, to allow -stim_times inputs to
be in milliseconds rather than seconds.
24 Mar 2009, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL)
Expand the -help output somewhat.
Based on feedback and confusion from the Dartmouth bootcamp.
24 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
by default now, no mask is applied in the scale and regression steps
Also added -regress_apply_mask option.
20 Mar 2009, RC Reynolds, @build_afni_Xlib, level 2 (MINOR), type 1 (NEW_PROG)
moved from X/@build.Xlib, for distribution
and added to SCRIPTS for building afni_src.tgz in Makefile.INCLUDE
19 Mar 2009, RC Reynolds, 1d_tool.py, level 3 (MAJOR), type 1 (NEW_PROG)
added lib_afni1D.py and 1d_tool.py
This is a library and tool for manipulating 1D files.
Many functions will still be added.
19 Mar 2009, RC Reynolds, eg_main_chrono.py, level 2 (MINOR), type 2 (NEW_OPT)
added -verbose_opts option, for being verbose during option processing
19 Mar 2009, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
a few additions and changes
- allow container chars (e.g. []) in decode_1D_ints()
- added is_valid_int_list()
- changed str vars to istr (as str is a keyword)
18 Mar 2009, RC Reynolds, eg_main_chrono.py, level 2 (MINOR), type 1 (NEW_PROG)
sample main python program using a library and chronological options
18 Mar 2009, DR Glen, 3dZcat, 3daxialize, level 2 (MINOR), type 2 (NEW_OPT)
NIFTI support
Fixed support for NIFTI output in 3dZcat and 3daxialize
Added -frugal option to 3daxialize to keep old behavior
for AFNI format datasets. Existing -frugal option in
3dZcat imposes 'oldish' behavior too.
16 Mar 2009, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
malloc extra val in case of percentile truncation
12 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
SUMA talks to matlab.
12 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
warn user about masking in orig space
- if despiking and no regression mask, apply -nomask
- added 'MASKING NOTE', to suggest no regresion mask until group space
12 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_reml_exec and -regress_3dD_stop
One can execute 3dREMLfit and/or 3dDeconvolve. Error blur is from each.
11 Mar 2009, RW Cox, 3dANOVA, level 2 (MINOR), type 2 (NEW_OPT)
Add -mask option to 3dANOVA, 3dANOVA2, 3dANOVA3
10 Mar 2009, RC Reynolds, NIfTI, level 1 (MICRO), type 5 (MODIFY)
added NIFTI_ECODEs 18-28 for the LONI MiND group
10 Mar 2009, DR Glen, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
Sum option
Sum option (for functional weighting of interiorosity measure)
09 Mar 2009, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT)
Add SPMG1 to -stim_times repertoire, and update help.
09 Mar 2009, RC Reynolds, suma-general, level 1 (MICRO), type 5 (MODIFY)
removed r_sprintf_long_to_hex from SUMA_Color.[ch]
09 Mar 2009, RC Reynolds, suma, level 1 (MICRO), type 2 (NEW_OPT)
added -motif_ver option
09 Mar 2009, RC Reynolds, 3dcalc, level 1 (MICRO), type 5 (MODIFY)
added edge/erode/dilate example to 3dcalc -help
06 Mar 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Add 'WAV' function (from waver) to -stim_times repertoire.
06 Mar 2009, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
if mri_automask_image() input is not really 3D, only apply clip
3dD uses automask for misfit warning, let this apply to niml.dset
06 Mar 2009, RC Reynolds, lesstif-general, level 1 (MICRO), type 5 (MODIFY)
motif/lesstif : put AFNI_MOTIF_TYPE in Xm.h.in : see 'afni -motif_ver'
05 Mar 2009, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
free vox_warp via KILL_list rather than directly when deleting dataset
Fixes afni crash: set acpc markers -> acpc view -> orig view
-> new markers -> acpc view -> death ...
05 Mar 2009, RC Reynolds, lesstif-general, level 1 (MICRO), type 5 (MODIFY)
init for every assignable argument to XtVaGetValues (12 files)
05 Mar 2009, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
init for every assignable argument to XtVaGetValues (19 files)
05 Mar 2009, RC Reynolds, @build.Xlib, level 1 (MICRO), type 2 (NEW_OPT)
change -noinstall option to -localinstall
04 Mar 2009, RW Cox, 3ddata.h, level 1 (MICRO), type 4 (BUG_FIX)
Fix usage of realpath() array dimension with RPMAX macro
04 Mar 2009, RC Reynolds, X-general, level 2 (MINOR), type 5 (MODIFY)
added openmotif build tree, updated @build.Xlib and README under X
04 Mar 2009, RC Reynolds, afni, level 1 (MICRO), type 2 (NEW_OPT)
added -motif_ver option
04 Mar 2009, RC Reynolds, @build.Xlib, level 1 (MICRO), type 2 (NEW_OPT)
added -noinstall option
03 Mar 2009, RC Reynolds, @build.Xlib, level 2 (MINOR), type 1 (NEW_PROG)
this is a build script for the local X packages
03 Mar 2009, RC Reynolds, xutil.c, level 1 (MICRO), type 5 (MODIFY)
another probably useless init (being cautious)
03 Mar 2009, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
modifed Makefile.linux_xorg7 and _64 for local X builds
02 Mar 2009, RW Cox, zfun, level 2 (MINOR), type 0 (GENERAL)
add compression functions (using zlib) to libmri in zfun.c
27 Feb 2009, RC Reynolds, X-general, level 2 (MINOR), type 5 (MODIFY)
added lesstif and libXt trees to cvs
20 Feb 2009, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
many inits to appease lesstif and Xt (w/Ziad)
13 Feb 2009, RW Cox, 3dRBFdset, level 1 (MICRO), type 0 (GENERAL)
Test program to make a dataset defined by RBF.
Mostly built to test the Radial Basis Function expansion functions in
mri_rbfinterp.c.
13 Feb 2009, RC Reynolds, dmat44.c, level 1 (MICRO), type 4 (BUG_FIX)
cut-and-paste error ...
13 Feb 2009, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
malloc changes: 5 more files
Friday the 13th, oooooooo... @ 18:31:30 EST: time will be 1234567890.
12 Feb 2009, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
added memsets following some malloc calls, or used calloc (14 files)
11 Feb 2009, RW Cox, 3dvolreg, level 2 (MINOR), type 4 (BUG_FIX)
replace DMAT_svdrot_old with DMAT_svdrot_newer
Old function fails sometimes, making the output rotation be garbage and
producing junk image results; the newer one seems more robust.
11 Feb 2009, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 5 (MODIFY)
removed duplicate -Rerrts option in output 3dREMLfit command
10 Feb 2009, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT)
Added -anim_dup to slow down movies
10 Feb 2009, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
fixed premature mask free-ing bug
09 Feb 2009, RW Cox, imseq.c, level 2 (MINOR), type 3 (NEW_ENV)
Add AFNI_ANIM_DUP environment variable.
Allows user to duplicate images when writting an animation (AGIF or
MPEG) file. A simple and stoopid way to slow down an MPEG.
09 Feb 2009, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 5 (MODIFY)
random updates, plus those for Fedora 10
09 Feb 2009, RC Reynolds, python-general, level 1 (MICRO), type 0 (GENERAL)
added new beginning-stage libraries lib_matplot.py and lib_wx.py
06 Feb 2009, RC Reynolds, NIFTI, level 1 (MICRO), type 5 (MODIFY)
added NIFTI_ECODE_PYPICKLE for MH; imported HJ's cast changes
05 Feb 2009, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
typo ==> DOF params for Full_Fstat weren't in output dataset
05 Feb 2009, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 5 (MODIFY)
added timing_tool.py use to sort times in example #7
04 Feb 2009, RC Reynolds, vol2surf, level 2 (MINOR), type 4 (BUG_FIX)
fixed norm reversal application and norm dir check computation
Thanks to Xiaopeng Zong for finding these problems.
04 Feb 2009, RC Reynolds, suma-general, level 1 (MICRO), type 5 (MODIFY)
update SUMA_paperplane.c and Makefile.solaris28_gcc for v1280 builds
Makefile now uses PREREQ=suma, gmake, -L/usr/dt/lib.
03 Feb 2009, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
No longer crashes with old format ROIs
03 Feb 2009, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed free-related error messages on OS X
These errors were generated because some pointers
were allocated with MCW_MALLOC and freed without it.
solution was to include mcw_malloc.h in coxplot and
gifti_choice.c
03 Feb 2009, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
fix machdep.h Makefile.solaris28_gcc for v1280 builds
02 Feb 2009, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT)
SurfDist now outputs distances from one node to a set of other nodes
02 Feb 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added load_col option to DriveSuma
02 Feb 2009, RW Cox, parser (calc programs), level 2 (MINOR), type 5 (MODIFY)
Add hrfbk4 and hrfbk5(t,T) functions to parser
To imitate the BLOCK4 and BLOCK5 response functions in 3dDeconvolve.
13 Jan 2009, ZS Saad, afni-matlab, level 2 (MINOR), type 1 (NEW_PROG)
Added GS_orth_1D.m to perform Gram-Schmidt orthogonalization
13 Jan 2009, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
AFNI should now be Lesstif compliant
Made numerous changes with Rick Reynolds. The biggest modification
regards buttons inside popup menus. Those buttons are no longer
inside rowcolumn widgets and had to be directly managed by afni.
08 Jan 2009, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
Added OpenMP directives as a test of multi-threading speedup.
07 Jan 2009, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Added more references to the help page.
07 Jan 2009, RC Reynolds, plug_crender, level 1 (MICRO), type 5 (MODIFY)
if lesstif, set threshold slider bar width
05 Jan 2009, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT)
Program no longer confined to FreeSurfer surfaces
The program now allows the user to specify any morph sphere,
not just sphere.reg or sphere. This required rewriting much of
of the program's main section but the algorithm for the mapping
remains unchanged.
05 Jan 2009, ZS Saad, CreateIcosahedron, level 1 (MICRO), type 2 (NEW_OPT)
Program uses new Spec writing function and writes different surface formats
05 Jan 2009, RW Cox, 3dAllineate, level 1 (MICRO), type 5 (MODIFY)
Change wsinc5 interpolation from radial to tensor product weight.
Speedup is about a factor of 6, which is worth the effort.
02 Jan 2009, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
Add '-final wsinc5' interpolation mode.
Slow but accurate. Weight function is 'designed' to reduce the variance
smoothing artifact.
02 Jan 2009, RC Reynolds, afni_environ.c, level 1 (MICRO), type 4 (BUG_FIX)
fixed bad lvalue when USE_TRACING is not defined
also fixed define for USE_TRACING in solaris and cygwin Makefiles
02 Jan 2009, RC Reynolds, Makefile, level 1 (MICRO), type 5 (MODIFY)
do not build balloon in Makefile.macosx_10.5_Intel_64 - libgsl is 32-bit
31 Dec 2008, RW Cox, 3dUndump, level 1 (MICRO), type 5 (MODIFY)
Make sure NaN values don't get into the dataset!
31 Dec 2008, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
fix for lesstif crash on 'where am i', along with ziad
30 Dec 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 5 (MODIFY)
For FALTUNG, use sparse matrix operations for pure least squares.
Deconvolution + penalty matrix is sparse. Uses the 'rcmat' functions
originally developed for 3dREMLfit. Speeds things up a lot when the
time series is long.
29 Dec 2008, RW Cox, 3dTfitter, level 1 (MICRO), type 0 (GENERAL)
Added better error messages if program runs out of memory.
24 Dec 2008, RC Reynolds, timing_tool.py, level 1 (MICRO), type 5 (MODIFY)
redefine 'sum' for older python versions
This also affects afni_util.py and make_random_timing.py.
23 Dec 2008, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
Program wouldn't read a -stim_times file that was all '*'
Actual change was in mri_read.c.
22 Dec 2008, G Chen, 3dICC.R, level 3 (MAJOR), type 1 (NEW_PROG)
IntraClass Correlation (ICC)
This is an R program that calculates ICC on 3D volume data based on a
two- or three-way random-effects ANOVA scheme. See more details at
http://afni.nimh.nih.gov/sscc/gangc/ICC
19 Dec 2008, RW Cox, 3dREMLfit, level 1 (MICRO), type 5 (MODIFY)
Added condition number checking and -GOFORIT
Also added floatscan checking for all output datasets, to be careful.
19 Dec 2008, DR Glen, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
Slice timing for children can be ignored
If child epi data does not need slice timing correction, script will
continue instead of exiting
16 Dec 2008, RW Cox, 3dREMLfit, level 1 (MICRO), type 0 (GENERAL)
Fixed bug in linear solution when #columns%4==3 (unrolling).
Actually in matrix.c, in function vector_multiply_transpose(), which is
only used in remla.c, which is only used in 3dREMLfit.c.
16 Dec 2008, G Chen, 3dGC.R, level 3 (MAJOR), type 1 (NEW_PROG)
Bivariate Granger causality analysis
This is an R program that runs Granger causality analysis with a
seed region versus the rest of the brain. See more details at
http://afni.nimh.nih.gov/sscc/gangc/3dGC
15 Dec 2008, RC Reynolds, Makefile, level 1 (MICRO), type 5 (MODIFY)
added USE_LESSTIF directive
Modified Makefile.linux_xorg7[_64], Makefile.macosx_10.5_Intel[_64].
13 Dec 2008, ZS Saad, afni-matlab, level 3 (MAJOR), type 1 (NEW_PROG)
RetroTS creates regressors for cardiac, respiratory, and RVT filtering
RetroTS.m and accompanying functions create slice-based regressors
for regressing out the effects of cardiac, respiratory, and RVT effects
from FMRI time series. The regressors generated are meant to be used
with 3dREMLfit.
11 Dec 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed -slibase bug.
Oopsie. -slibase didn't work properly with more than 1 added column per
slice. Also, per the request of ZSS, you can now input more than 1
column set per image file, in repetitive slice order:
0 1 2 3 0 1 2 3 0 1 2 3
if there are 4 slices in the dataset, for example.
11 Dec 2008, RW Cox, 3dREMLfit, level 1 (MICRO), type 5 (MODIFY)
Should behave better with ocllinear regression matrix.
Modified the QR decomposition to adjust 'tiny' diagonal elements of R,
to avoid division by zero (or near-zero). Prints a warning message when
this adjustment is made.
10 Dec 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added new options for extra stimuli, RONI and an external volreg base
- allow NIfTI datasets as input (but process as AFNI)
- added -regress_extra_stim_files and -regress_extra_stim_labels
- added -regress_RONI and -volreg_base_dset (for Jill Weisberg)
09 Dec 2008, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed (potential) SUMA crash when Draw ROI interface is first opened
09 Dec 2008, ZS Saad, @Align_Centers, level 2 (MINOR), type 2 (NEW_OPT)
Added -cm option to allow centering based on the center of mass
09 Dec 2008, ZS Saad, 3dCM, level 1 (MICRO), type 5 (MODIFY)
Added history note to 3dCM
09 Dec 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
Added 'dmBLOCK' to the '-stim_times_IM' repertoire.
08 Dec 2008, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
SUMA works now with LESSTIF, interface is almost the same as in MOTIF
08 Dec 2008, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL)
Expand -stim_times_AM modulation abilities even more.
Now allow 'duration modulation' via the 'dmBLOCK' response model. A
general facility for allowing up to 3 nonlinear function parameters has
been built into the code, for future expansion. 'dmBLOCK' can also be
amplitude modulated.
08 Dec 2008, RC Reynolds, xmat_tool.py, level 1 (MICRO), type 5 (MODIFY)
allow -test_libs to proceed without numpy
08 Dec 2008, RC Reynolds, Makefile, level 1 (MICRO), type 0 (GENERAL)
added Makefile.macosx_10.5_G4
05 Dec 2008, DR Glen, to3d, level 2 (MINOR), type 5 (MODIFY)
Siemens DICOM handling
added -oblique_origin and -reverse_list to help handle Siemens
DICOM data. oblique_origin option added to to3d and 3drefit
Rick added flipped slice handling to oblique mosaic handling
04 Dec 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Extend -stim_times_AM2 option to allow multiple amplitudes
04 Dec 2008, RW Cox, 1dMarry, level 2 (MINOR), type 5 (MODIFY)
Allow multiple marriages, to go with 3dDeconvolve changes
04 Dec 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
added balloon target for M Belmonte
Also modified Makefile.linux_xorg7_64 and macosx_10.4_G5/Intel and 5_Int*.
04 Dec 2008, RC Reynolds, balloon, level 1 (MICRO), type 1 (NEW_PROG)
new program by M Belmonte
02 Dec 2008, ZS Saad, SpharmReco, level 3 (MAJOR), type 1 (NEW_PROG)
Reconstructs data from spherical harmonics decomposition.
See SpharmDeco -help and the demo script @Spharm.examples
for details.
02 Dec 2008, ZS Saad, SpharmDeco, level 3 (MAJOR), type 1 (NEW_PROG)
Performs spherical harmonics decomposition.
This program performs spherical harmonics decomposition
for surfaces' geometry and/or surface-based data
See SpharmReco -help and the demo script @Spharm.examples
for details.
02 Dec 2008, ZS Saad, @Spharm.examples, level 3 (MAJOR), type 1 (NEW_PROG)
A script to demonstrate the usage of SpharmDeco and SpharmReco
02 Dec 2008, ZS Saad, @NoisySkullStrip, level 3 (MAJOR), type 1 (NEW_PROG)
A script to improve skull stripping in noisy of heavily shaded data
02 Dec 2008, ZS Saad, general, level 1 (MICRO), type 4 (BUG_FIX)
Environment vars. set in the shell override those in .afnirc or .sumarc
01 Dec 2008, RC Reynolds, timing_tool.py, level 3 (MAJOR), type 1 (NEW_PROG)
a tool for manipulating and evaluating stimulus timing files
This is useful for getting statistics on rest timing.
01 Dec 2008, RC Reynolds, option_list.py, level 1 (MICRO), type 5 (MODIFY)
added 'opt' param to more get_* functions
01 Dec 2008, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 5 (MODIFY)
moved min_mean_max_stdev to afni_util.py and modified help examples
24 Nov 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added options -infile_list and -show_sorted_list
The -show_sorted_list option will print a list of files by run/index.
21 Nov 2008, ZS Saad, @fast_roi, level 3 (MAJOR), type 1 (NEW_PROG)
Creates Atlas-based ROIs in original space for real-time experiments
21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added Options menu, Show Cosmat and GUI help
This is the initial release version, 1.0.
21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -test_libs option
21 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT)
removed 'R' from basic test list, and applied verb 2 to base usage
20 Nov 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
incorportated real-time volume writing from V. Roopchansingh of MCW
18 Nov 2008, RW Cox, 3dANOVA programs, level 2 (MINOR), type 2 (NEW_OPT)
Add option to output float-valued datasets.
Set the AFNI_FLOATIZE environment variable to YES, and the output of
3dANOVA, 3dANOVA2, and 3dANOVA3 will be stored in float format instead
of in scaled short format. [Per the request of Paul Hamilton]
18 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -test, -show_col_types, -show_cosmat, -show_fit_ts, -cormat_cutoff
also added the main help
18 Nov 2008, RC Reynolds, afni_xmat.py, level 1 (MICRO), type 5 (MODIFY)
added extra_cols param to make_show_conds_str
14 Nov 2008, RW Cox, help_format, level 1 (MICRO), type 1 (NEW_PROG)
For formatting -help output into Web pages with hyperlinks.
To be used with the dist_help script for making the help Web pages from
the -help outputs of all AFNI programs.
13 Nov 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added a NIDO sphere as Displayable Object
See suma -help_nido for details.
13 Nov 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -al option to use 3dAllineate -lpa
11 Nov 2008, RW Cox, 3dREMLfit, level 1 (MICRO), type 0 (GENERAL)
-usetemp now also saves output dataset stuff to TMPDIR.
10 Nov 2008, RW Cox, 3dUndump, level 1 (MICRO), type 5 (MODIFY)
Add warning if non-integer values are being saved to shorts/bytes.
07 Nov 2008, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Write Clust_table.1D into dataset directory, not startup directory.
07 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 5 (MODIFY)
more updates:
- scipy is only tested for when necessary
- compute norms locally if no scipy
- solve_against_1D, linear_combo: return error string instead of code
- added -chrono option, to make all options chronological
(so options are essentially scriptable)
07 Nov 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
tlrc view handling
fixed view name of tlrc output with tlrc_master set to SOURCE
06 Nov 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 0 (GENERAL)
Add 'scale to shorts misfit' warning messages.
Also added to 3dcalc and some other programs.
06 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
pre-release updates:
- added many initial command-line options
- added plot_xmat_as_one toggle button
- added computation of cosine matrix and cosmat_warnings
- separated GUI code into new file gui_xmat.py
06 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -full_test
06 Nov 2008, RC Reynolds, option_list.py, level 1 (MICRO), type 2 (NEW_OPT)
added opt param to get_type_opt and get_type_list
had to modify calls in make_random_timing.py and gen_epi_review.py
06 Nov 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Oblique children handling
fixed combination of oblique with child epis for epi2anat output
05 Nov 2008, RW Cox, model_expr2.c, level 1 (MICRO), type 0 (GENERAL)
Modified to allow up to 9 parameters -- see code for details.
05 Nov 2008, RW Cox, 3dREMLfit, level 1 (MICRO), type 0 (GENERAL)
If it saves memory, convert dataset to new MRI_vectim format.
That is, an array of time series vectors, of voxels in the mask. Will
save memory if the number of voxels in the mask is less than 1/2 the
volume.
04 Nov 2008, RW Cox, 3dNLfim, level 2 (MINOR), type 0 (GENERAL)
Added model_expr2.c
Model that uses an arbitrary 3dcalc-like expression with 2 free
parameters (any letters but 't', which is used for the time axis).
04 Nov 2008, RW Cox, 3dBlurToFWHM, level 2 (MINOR), type 4 (BUG_FIX)
skip all zero sub-bricks in the blurmaster - for Tomski Rosski
04 Nov 2008, RC Reynolds, vol2surf, level 1 (MICRO), type 5 (MODIFY)
only complain about statsym_string in debug mode
04 Nov 2008, RC Reynolds, plug_vol2surf, level 1 (MICRO), type 5 (MODIFY)
fail if NIML output dataset does end in .niml.dset
04 Nov 2008, RC Reynolds, 3dVol2Surf, level 1 (MICRO), type 5 (MODIFY)
fail if NIML output dataset does end in .niml.dset
03 Nov 2008, ZS Saad, 3dNLfim, level 1 (MICRO), type 2 (NEW_OPT)
Added Exp (single exponential) model
03 Nov 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Several changes
Finished -gltsym, -Rglt, and -Oglt options = add GLTs on the 3dREMLfit
command line and output those exclusively to new files.
Modified -addbase and -slibase to do censoring if input 1D files are the
same length as the uncensored matrix.
Also fixed bugs in -ABfile. Oopsie.
31 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_timing_stats option
Also, made a small change affecting timing (old results will not match).
31 Oct 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
moved functions encode_1D_ints and decode_1D_ints here
31 Oct 2008, DR Glen, 3drefit, level 2 (MINOR), type 5 (MODIFY)
Time axis attributes
Added support in 3drefit for applying time axis attributes
30 Oct 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
AddEdge with epi2anat
fixed AddEdge option for epi2anat output
29 Oct 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 5 (MODIFY)
if the X-matrix has a constant regressor, do not de-mean it
In such a case, the cormat would not exactly be a correlation matrix.
29 Oct 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 1 (NEW_PROG)
program to test python module imports (interface to module_test_lib.py)
28 Oct 2008, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
add '3' checkerboard (inverse stippling to '#' key)
28 Oct 2008, RC Reynolds, module_test_lib.py, level 2 (MINOR), type 1 (NEW_PROG)
library to test python module imports
One might want to apply this module at the top of any python file.
28 Oct 2008, RC Reynolds, xmat_tool.py, level 1 (MICRO), type 5 (MODIFY)
use module_test_lib to test imports
27 Oct 2008, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Checkerboard underlay and overlay images
For Ziad -- to help judge image alignment. Use the # key to turn
checkerboarding on and off. The grayscale intensity bar popup menu has
a new sub-menu to select the check size in units of underlay pixels. At
this time, checkerboarding does NOT work with image Save, RowGraphs, or
SurfGraph, or just about any other feature. If you want a picture of a
checkerboarded image, you'll have to use a snapshot utility to grab the
window.
27 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -offset option
27 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX)
actually applied -min_rest, sorry...
27 Oct 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_motion_file option
24 Oct 2008, RC Reynolds, xmat_tool.py, level 4 (SUPER), type 1 (NEW_PROG)
program to inspect a .xmat.1D X-matrix, possibly against a time series
This is a Graphical tool for plotting a design matrix, reviewing
condition numbers or the correlation matrix, and fitting to a 1D
time series.
23 Oct 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Added -rout option, by popular 'demand'
23 Oct 2008, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Add MDF estimate to FDR q-value
MDF = Missed Detection Fraction = estimate of what fraction of true
positives are below any given threshold (analogous to FDR = estimate of
what fraction of above threshold voxels are true negatives). Displays
in the hint attached to the label below the threshold slider. Purely
experimental, since estimating the number of true positives in a given
collection of p-values is not a well-defined concept by any means.
23 Oct 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 4 (BUG_FIX)
removed reference to cdflib, for 'make afni_src.tgz'
23 Oct 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
added lists_are_same function
20 Oct 2008, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
added write_text_to_file function
20 Oct 2008, RC Reynolds, afni_driver.c, level 2 (MINOR), type 2 (NEW_OPT)
added 'GETENV' to the list of DRIVE_AFNI commands
17 Oct 2008, ZS Saad, imcat, level 1 (MICRO), type 2 (NEW_OPT)
-crop is a new option for cropping an image
16 Oct 2008, RC Reynolds, thd_mastery, level 1 (MICRO), type 5 (MODIFY)
THD_copy_dset_subs should not need to add a warp structure
15 Oct 2008, RW Cox, fdrval, level 2 (MINOR), type 1 (NEW_PROG)
Compute FDR value on command line, from dataset header
15 Oct 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed errts (etc) outputs: censored values not set to zero!
15 Oct 2008, DR Glen, afni plugouts, @AddEdge, level 2 (MINOR), type 5 (MODIFY)
quiet communications
@AddEdge silences communications as plugout
14 Oct 2008, RW Cox, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
If source=scaled shorts, then output will be scaled as well.
14 Oct 2008, RC Reynolds, thd_mastery, level 1 (MICRO), type 5 (MODIFY)
verify sub-brick list in THD_copy_dset_subs()
14 Oct 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
added wrap string param to add_line_wrappers (to wrap with newlines)
14 Oct 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor updates
AddEdge option enhanced and help updated
14 Oct 2008, DR Glen, @AddEdge, level 2 (MINOR), type 5 (MODIFY)
Help and options
More user options, improved help, removed temporary files
09 Oct 2008, G Chen, 1dGC.R, level 4 (SUPER), type 1 (NEW_PROG)
Multivariate Granger causality analysis
This is an R program that runs Granger causality analysis among a few
pre-select regions. See more details at
http://afni.nimh.nih.gov/sscc/gangc/1dGC
08 Oct 2008, RC Reynolds, NIFTI, level 1 (MICRO), type 5 (MODIFY)
allow cbl with indices in 0..nt*nu*nv*nw-1
07 Oct 2008, RC Reynolds, NIFTI, level 1 (MICRO), type 5 (MODIFY)
added nifti_NBL_matches_nim() check for write_bricks()
06 Oct 2008, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
FDR curves can now be fetched from warp_parent
If a func dataset is missing FDR curves, then the program tries to get
them from the warp_parent dataset. Also, AFNI no longer allows you to
add FDR curves to a dataset without actual bricks (warp-on-demand).
06 Oct 2008, DR Glen, 3drefit, level 2 (MINOR), type 5 (MODIFY)
-atrfloat and -atrint options
Allows addition and modification of dataset attributes
including modifying IJK_TO_DICOM_REAL. Not all attributes
can be modified if fairly basic to dataset.
03 Oct 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
SUMA accepts text, images, and textures as Displayable Objects
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects (DOs). The new DOs are in a simple
NIML format. It is simplest to look at the script @DO.examples
for illustrations of the various forms of DOs that SUMA supports.
Sample NIML DOs (called NIDOs) are now provided with the distribution
They are called demo.*.niml.do.
03 Oct 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
-viewer_position/_width/_height/_size to control window placement
See DriveSuma -help for details.
03 Oct 2008, ZS Saad, @DO.examples, level 2 (MINOR), type 1 (NEW_PROG)
A script that demonstrates the use of Displayable Objects
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects (DOs).
03 Oct 2008, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_StartUpLocation to control initial window placement
See output for suma -environment for details.
02 Oct 2008, RC Reynolds, GIFTI, level 1 (MICRO), type 5 (MODIFY)
minor changes
- separate diffs in DAs from those in gifti_image
- decode additional data types: INT8, UINT16, INT64
- add link flags to libgiftiio_la target
30 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -gltsym option
Makes it easy for the user to add GLTs without using 3dDeconvolve.
29 Sep 2008, RC Reynolds, 3dmatmult, level 3 (MAJOR), type 1 (NEW_PROG)
program to multiply AFNI datasets slice-by-slice as matrices
26 Sep 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
-child_anat option
Convenience option to align follower anat datasets to epi
25 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -usetemp option
Saves REML setup matrices for various cases to tmp disk files. Is
necessary for -slibase and -Grid 5 combined, if anyone ever actually
wants to run such a case.
24 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
-addbase and -slibase options to add baseline columns to matrix
In particular, -slibase is intended for per-slice modeling of
physiological noise effects. Sucks up a lot of memory and CPU time.
23 Sep 2008, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
save last jumpto_xyz string, etc.
23 Sep 2008, RC Reynolds, gen_epi_review.py, level 2 (MINOR), type 5 (MODIFY)
in script, check for existence of given datasets
23 Sep 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -remove_preproc_files option (akin to -move_preproc_files)
22 Sep 2008, RW Cox, 3dREMLfit, level 1 (MICRO), type 0 (GENERAL)
got rid of some big memory leaks
19 Sep 2008, RW Cox, NIML library, level 1 (MICRO), type 0 (GENERAL)
modify NI_alter_veclen to allow conversion to non-empty from empty
19 Sep 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
-giant_move option
For data that are very far apart
Fixed bug using long path names
18 Sep 2008, RW Cox, Vecwarp, level 1 (MICRO), type 4 (BUG_FIX)
Only require +orig dataset if user actually NEEDS it
Program required the +orig version of the -apar dataset, which is needed
for SureFit work, even if it wasn't actually going to be used. Not any
more.
18 Sep 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
More options
Intermediate file saved optionally now,
partial_axial,sagittal,coronal options
Edge-based method, nocmass default, resample step optional,
Added options to support searching for smaller structures,
3dWarpDrive can be used optionally as volume registration program
prep_off option to turn off several preprocessing steps
AddEdge option uses simplified names in output in new directory
17 Sep 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 2 (NEW_OPT)
added -labels option, for including labels in filenames
16 Sep 2008, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT)
-node_path_do outputs the shortest path between two nodes
The shortest path(s) are stored as a SUMA Displayable Object
which can be loaded into SUMA with ctrl+alt+s or using DriveSuma.
16 Sep 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
-load_do sends SUMA Displayable Objects to be rendered
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects.
16 Sep 2008, RW Cox, 3dDeconvolve, level 1 (MICRO), type 5 (MODIFY)
Made 3dREMLfit command echo more complete for user's convenience
16 Sep 2008, RC Reynolds, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
allow attribute editing of NIfTI datasets
15 Sep 2008, RW Cox, Draw Dataset plugin, level 2 (MINOR), type 5 (MODIFY)
Keystrokes F3 and F3 now decrement/increment drawing value in plugin
10 Sep 2008, RW Cox, 3dTfitter, level 1 (MICRO), type 5 (MODIFY)
skip all zero voxels; add voxel ID to error messages
10 Sep 2008, RC Reynolds, plug_realtime, level 1 (MICRO), type 4 (BUG_FIX)
re-added sending of magic_bye string on MP socket close
09 Sep 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 5 (MODIFY)
add savehist to allcost output
03 Sep 2008, RC Reynolds, plug_realtime, level 1 (MICRO), type 5 (MODIFY)
moved drive_wait execution to RT_tell_afni
02 Sep 2008, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 4 (BUG_FIX)
Starting sphere center was incorrectly initialized
02 Sep 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 2 (NEW_OPT)
-allcostX1D option (for Chairman Z)
02 Sep 2008, RC Reynolds, GIFTI, level 1 (MICRO), type 5 (MODIFY)
have distribution Makefiles build with GIFTI/expat/zlib
29 Aug 2008, ZS Saad, ExamineXmatR, level 3 (MAJOR), type 1 (NEW_PROG)
An interactive tool to examine a design matrix
29 Aug 2008, ZS Saad, 3ddelay, level 2 (MINOR), type 4 (BUG_FIX)
Unitialized pointer in 3ddelay
29 Aug 2008, ZS Saad, afni-general, level 1 (MICRO), type 0 (GENERAL)
Added toy programs 3dTsmoothR.c and toyR.c to test C<-->R interface
The programs demonstrate how to call R functions from C.
To build them one needs to run tcsh ./@RmakeOpts
Add 'include Makefile.R.INCLUDE' to Makefile
Then make 3dTsmoothR toyR
The programs demonstrate time series processing and plotting in R.
29 Aug 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
More small changes, to speed the program up a little
* reduce the number of function evals used in the coarse refinements
* after coarse refinements, cast out parameter sets that are very close
to the best set, to avoid duplicative work at the fine pass
29 Aug 2008, RC Reynolds, vol2surf, level 2 (MINOR), type 5 (MODIFY)
fill in COLMS_STATSYM attribute when writing .niml.dset dataset
29 Aug 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
Feature size, AddEdge, skullstrip,rat options
Added options to support searching for smaller structures,
an option for rat brain alignment, alternate options for 3dSkullstrip
and an optional call for @AddEdge
28 Aug 2008, RW Cox, 3dAllineate, level 3 (MAJOR), type 5 (MODIFY)
A number of changes to improve robustness.
* Don't smooth noise added to source image outside of the mask
* Reduce default smoothing level for -lpc in coarse pass
* Increase number of points used for matching in the coarse pass
* More refinements of the twobest results in the coarse pass
* Refinements (-num_rtb option) of the twobest results in the fine pass
All this adds CPU time, but seems to make the program more reliably
convergent. Also:
* Restored operation of the -check option, to restart the optimization
at the final solution with other methods, to see what results they
give compared to the original method.
28 Aug 2008, RW Cox, miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Fixed 'is used uninitialized' errors in several codes.
Via the new macro ZZME() in 3ddata.h, which zeros out a struct.
27 Aug 2008, DR Glen, 3danisosmooth, level 2 (MINOR), type 4 (BUG_FIX)
Initialized variable for 3D case
26 Aug 2008, RW Cox, 3dTcorrMap, level 2 (MINOR), type 1 (NEW_PROG)
Average correlations with every other voxel time series.
Kind of slow. For Kyle Simmons. And I still don't recognize Missouri!
26 Aug 2008, RC Reynolds, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
initialized ntask in all cases
25 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Added residual outputs to 3dREMLfit.
22 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add FDR curves and -?fitts options.
22 Aug 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added DRIVE_WAIT command string
The command will be executed after the first volume is processed,
which is good for opening windows appropriate to a new dataset.
22 Aug 2008, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT)
added -drive_wait option
21 Aug 2008, RW Cox, 3dREMLfit, level 4 (SUPER), type 1 (NEW_PROG)
Program to mimic 3dDeconvolve, but with serial correlations
Uses ARMA(1,1) model of noise, separately for each voxel.
21 Aug 2008, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
in edt_dsetitems, if storage mode can be inferred from prefix, apply it
21 Aug 2008, RC Reynolds, afni, level 2 (MINOR), type 2 (NEW_OPT)
added -disable_done option to safeguard real-time mode
21 Aug 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
use DSET_BRIKNAME for dataset control, as that is updated for smode
21 Aug 2008, RC Reynolds, Dimon, level 1 (MICRO), type 5 (MODIFY)
updated help and suggest -num_slices with -sleep_init
18 Aug 2008, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL)
add -force_TR option to override input dataset TR from header
Also added a printout of the dataset TR if the PSFB warning gets
printed.
18 Aug 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
increase DRIVE_LIMIT to 4Kb, read env vars each run
These variables can now be controlled through drive_afni 'SETENV'
(either via 'plugout_drive' or 'Dimon -drive_afni'):
- AFNI_REALTIME_Mask_Vals : specify what gets sent to serial_helper
- AFNI_REALTIME_SHOW_TIMES : specify whether to show data timestampts
- AFNI_REALTIME_SEND_VER : specify whether to send comm version
15 Aug 2008, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
init graph->grid_spacing, to prevent potential div by 0 via DRIVE
14 Aug 2008, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
do not automatically print -max along with -var
14 Aug 2008, RC Reynolds, Dimon, level 1 (MICRO), type 5 (MODIFY)
moved num_slices check to separate function
05 Aug 2008, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
re-added the un16 fix from July 1
03 Aug 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 5 (MODIFY)
added swap ability for ANALYZE 7.5 format, and made swapping complete
- added nifti_analyze75 struct
- modified swap_nifti_header to swap all fields (analyze or nifti)
- added regression testing script c16.rand.swap
These changes were motivated by C Burns.
03 Aug 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -help_ana, -disp_ana, -swap_as_analyze, -swap_as_nifti, -swap_as_old
31 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 2 to work as -disp_all
See 'HELLO versions' from 'serial_helper -help' for details.
See 'example E' from 'Dimon -help' for a complete testing example.
31 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
enhancements to communication with serial helper
- added 'Motion Only' to methods
- parameter methods can easily be switched per run
- SEND_VER replaces HELLO_VER as Y/N variable
31 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -num_slices option, and full real-time example E
30 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 1 and -show_times option
30 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 1 and show_times option
These are set via AFNI_REALTIME_SEND_VER and AFNI_REALTIME_SHOW_TIMES.
30 Jul 2008, DR Glen, 3dinfo.c, level 1 (MICRO), type 5 (MODIFY)
Exit codes set to 1 on error
29 Jul 2008, ZS Saad, afni, level 2 (MINOR), type 5 (MODIFY)
Changed transform used to crete mni coord. in interactive whereami
The transform from TLRC to MNI used to be via the manually TLRCed
N27 brain. However this created inconsistency in the second line of the
Focus point output (MNI Brain) on the order of a couple of mm
with the command-line whereami program.
Now both interactive and command-line whereami produce the same
Focus Point output. Note that the rest of the whereami
output remains unchanged.
29 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 5 (MODIFY)
captured and output more signal and error info, flushed output buffer
29 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
print more socket error info, send MP vals w/out mask
28 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 4 (BUG_FIX)
alter check for bad socket: use tcp_alivecheck over tcp_writecheck
28 Jul 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
Pre and post transformation matrices
Allow pre-transformation matrix instead of oblique transformation
and post-transformation instead of tlrc transformation.
Fixed concatenated matrices for oblique data. Master options
allow specification of dimension size on output. Script arguments
saved in output dataset.
25 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
allow -sleep_vol to be very small without early run termination
23 Jul 2008, RC Reynolds, 3dttest, level 2 (MINOR), type 2 (NEW_OPT)
added -base1_dset option, where -base1 value can vary over voxels
Added for M Beauchamp.
18 Jul 2008, RC Reynolds, 3dNLfim, level 2 (MINOR), type 5 (MODIFY)
listed signal and noise models in -help output
18 Jul 2008, DR Glen, to3d, level 2 (MINOR), type 5 (MODIFY)
Reverse order of slices in Siemens Mosaic data
Some Siemens Mosaic data can be in reverse order depending upon
obscure Siemens private DICOM tags.
Thanks to Doug Greve in Freesurfer group for edifying this situation
17 Jul 2008, RC Reynolds, 3dNLfim, level 2 (MINOR), type 5 (MODIFY)
warn the user if DSET_NVALS is not the same as DSET_NUMTIMES
That would suggest the dataset has no time axis.
16 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added -disp_all to give formatted display of 'all' mask data
This was added for P Kundu.
16 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added choice of 'Vals to Send' to serial_helper
Can now send index,i,j,k,x,y,z,value for every value in mask.
15 Jul 2008, RW Cox, count, level 1 (MICRO), type 4 (BUG_FIX)
Make '-suffix' work correctly for last item (per Fred Tam).
Also, make '-sep' and '-suffix' work as separate items,
instead of as synonyms for the same thing, which is stoopid.
15 Jul 2008, DR Glen, general, level 2 (MINOR), type 5 (MODIFY)
Can turn off all obliquity warnings
AFNI_NO_OBLIQUE_WARNING variable is extended to turn off warnings
about using oblique data in commandline programs and in GUI
15 Jul 2008, DR Glen, 3dWarp, level 2 (MINOR), type 4 (BUG_FIX)
Print correct obliquity transformation matrix
14 Jul 2008, RW Cox, 3dDeconvolve, level 1 (MICRO), type 5 (MODIFY)
Add 'RunStart' field to xmat.1D output, to indicate start of runs.
14 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
terminate TCP transmission to serial_helper if mask is bad
14 Jul 2008, RC Reynolds, afni_history, level 2 (MINOR), type 5 (MODIFY)
a single integer option is interpreted as with -past_entires
14 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -sleep_init, -sleep_vol, -sleep_frac
These options control the timeout periods between data checks.
11 Jul 2008, RC Reynolds, Dimon, level 1 (MICRO), type 5 (MODIFY)
include last 4 elements of obl_matrix, even though probably useless
10 Jul 2008, RC Reynolds, plug_realtime, level 3 (MAJOR), type 5 (MODIFY)
receive oblique transform matrix via new OBLIQUE_XFORM interface
10 Jul 2008, RC Reynolds, Dimon, level 3 (MAJOR), type 5 (MODIFY)
if the data is oblique, pass the transformation matrix to plug_realtime
09 Jul 2008, RC Reynolds, plug_realtime, level 1 (MICRO), type 5 (MODIFY)
if user closes graph window, allow comm with serial_helper to proceed
07 Jul 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
move extra newline from args_as_command to show_args_as_command
03 Jul 2008, RW Cox, matrix.c, level 1 (MICRO), type 5 (MODIFY)
Add QR function matrix_qrr() to matrix.c library file.
03 Jul 2008, RC Reynolds, plug_drawdset, level 1 (MICRO), type 4 (BUG_FIX)
edt_dset_items.c: for .hdr, use .img brick file, storage_mode = BY_NIFTI
02 Jul 2008, RC Reynolds, Dimon, level 1 (MICRO), type 5 (MODIFY)
provide suggestions in the case of a real-time TCP connection failure
01 Jul 2008, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
fixed crash in case of mosaic and un16, no longer having im data
Problem found by R. McColl.
01 Jul 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
modified the make system for building programs in the install directory
- modified Makefile.INCLUDE's INFLAGS and ISFLAGS
- modified SUMA_INPATH in SUMA_Makefile_NoDev.
- removed 'rickr/' dirs from includes in mrilib.h, plug_crender.c and
3dAllineate.c
Requested by V. Roopchansingh of MCW.
30 Jun 2008, RC Reynolds, gen_epi_review.py, level 2 (MINOR), type 5 (MODIFY)
make script executable, decrease sleep, add usage comment in script
30 Jun 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -gen_epi_review and -no_epi_review options
By default, a drive_afni script to review EPI data is now generated.
27 Jun 2008, RC Reynolds, gen_epi_review.py, level 3 (MAJOR), type 1 (NEW_PROG)
generate afni/drive_afni script to review initial EPI data
This program was written to be called from the afni_proc.py output script.
27 Jun 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
small modification to find_command_end
25 Jun 2008, RC Reynolds, howto, level 2 (MINOR), type 5 (MODIFY)
put disclaimers at the tops of HowTo #1, #2, and #5
references to current AFNI class handouts were included
25 Jun 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -past_entries option
24 Jun 2008, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Extend max number of clusters reportable, for Shruti.
24 Jun 2008, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
added the ability to output 1D iresp datasets
20 Jun 2008, RC Reynolds, libmri, level 2 (MINOR), type 5 (MODIFY)
thd_niftiread: do not scale to float if scale=1 and inter=0
19 Jun 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 5 (MODIFY)
help update, added -show_valid_opts, use '*' as separator w/amplitudes
19 Jun 2008, RC Reynolds, file_tool, level 1 (MICRO), type 5 (MODIFY)
removed printing of pointers in disp_ functions
18 Jun 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixes - duplicate master options, mislabeled variable
16 Jun 2008, RC Reynolds, file_tool, level 2 (MINOR), type 5 (MODIFY)
show output for multiple bad files when using -show_bad_backslash
13 Jun 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 2 (NEW_OPT)
added nifti_compiled_with_zlib()
13 Jun 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -with_zlib, and ability to add extensions via 'file:FILENAME'
extension update added for J. Gunter
13 Jun 2008, RC Reynolds, 3dclust, level 2 (MINOR), type 5 (MODIFY)
in the help, Volume defaults to microliters, unless -dxyz=1 is used
12 Jun 2008, RC Reynolds, neuro_deconvolve.py, level 2 (MINOR), type 1 (NEW_PROG)
generate 3dTfitter script to deconvolve a BOLD signal into a neuro signal
12 Jun 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
added get_dset_reps_tr, get_default_polort, get_dset_reps_tr, max_dim_1D
also, updated find_last_space to deal with long strings
12 Jun 2008, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
shifted code to afni_util.get_dset_reps_tr and .get_default_polort
11 Jun 2008, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 5 (MODIFY)
Obliquity handling in alignment, more grid options
11 Jun 2008, DR Glen, afni_base.py, level 1 (MICRO), type 5 (MODIFY)
Added isFloat method to python support
11 Jun 2008, DR Glen, 3dWarp.c, level 1 (MICRO), type 5 (MODIFY)
Prints oblique transformation matrix
10 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 2 (NEW_OPT)
Add -ARMA option to estimate ARMA(1,1) parameters
06 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation matrix of a time series, averaged locally.
06 Jun 2008, RW Cox, 3dErrtsCormat, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation matrix of a time series, globally.
06 Jun 2008, RC Reynolds, plug_crender, level 2 (MINOR), type 4 (BUG_FIX)
integral threshold was off by 1
06 Jun 2008, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 5 (MODIFY)
get_*_opt now returns an error code
03 Jun 2008, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Made AFNI_IMAGE_TICK_DIV_IN_MM editable (in 'Edit Environment')
This is Rick's method for putting a physical scale around the edge of an
image. Of course, you have to use the grayscale intensity bar popup
menu to actually put the tick marks on. This just converts the
'division' count to mm.
02 Jun 2008, RC Reynolds, model_demri_3, level 1 (MICRO), type 5 (MODIFY)
small help update to clarify residual C curve input
02 Jun 2008, RC Reynolds, GIFTI, level 1 (MICRO), type 0 (GENERAL)
added CMakeLists.txt and XMLCALL update from Simon Warfield
also added LICENSE.gifti
29 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 5 (MODIFY)
allowed for -polort -1 and for sub-brick selection with dataset names
29 May 2008, RC Reynolds, model_demri_3, level 1 (MICRO), type 4 (BUG_FIX)
help update to clarify use of AFNI_MODEL_D3_R1I_DSET
22 May 2008, RC Reynolds, 3dTshift, level 2 (MINOR), type 4 (BUG_FIX)
with -rlt, slices without any time shift must still be processed
problem noticed by Jie Huang
21 May 2008, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Put -1dindex into '3dclust' output from Clusterize report. Oops.
21 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed incorrect scaling in Cp computation
The error was introduced on April 8, 2008.
21 May 2008, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 2 (NEW_OPT)
added -amplitudes option (for Rutvik Desai)
20 May 2008, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
Clusterize: '-' as the filename means write to stdout.
20 May 2008, RW Cox, plugout_drive, level 1 (MICRO), type 2 (NEW_OPT)
Make TCP/IP to 'localhost' the default. Add option '-shm' if needed.
20 May 2008, RW Cox, afni_cluster.c, level 1 (MICRO), type 0 (GENERAL)
Added BHelp to a bunch of buttons.
18 May 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added options for TR-locking and storing '3dDeconvolve -nodata' examples
- added shuffle() to replace that from random (cannot produce all perms)
- added options -tr, -tr_locked and -save_3dd_cmd
- changed -stim_time option to -stim_dur
18 May 2008, RC Reynolds, afni_history, level 1 (MICRO), type 5 (MODIFY)
sped up comparison (since histories have gotten long)
17 May 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
check result of 3dDeconvolve execution in output script
If 3dDeconvolve fails, terminate the script so that the user can
see what happened.
15 May 2008, ZS Saad, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
added -n_rand and -n_randseed
15 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 4 (BUG_FIX)
Fixed memory corruption when using more than 20 regressors
15 May 2008, RW Cox, thd_initdblk.c, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_IGNORE_BRICK_FLTFAC = YES means ignore brick factors on input
This is a quick hack for Ziad, and must be used with care! Example:
3dBrickStat -DAFNI_IGNORE_BRICK_FLTFAC=YES -max -slow fred+orig
14 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed application of decay term
14 May 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
1D file names for child epi data,micro changes
13 May 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -set_extern_filelist option, and help for using external data files
13 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
gifticlib-1.0.0: initial release
includes support for (set/clear/read/write) external data files
09 May 2008, ZS Saad, 3dROIstats, level 3 (MAJOR), type 2 (NEW_OPT)
Added option -1Dformat to output results in 1D format
09 May 2008, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Modify PUTENV macro to malloc new string for each variable
Previously used an array str[256] that would go away, and that's
actually not legal in Linux -- the array must be permanent, since its
pointer is what gets put in the environment, not a copy of the string.
That's why the PUTENV didn't work on Linux (but worked for some reason
on Mac OS X)! Sheesh.
09 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
gifticlib-0.0.18: giiCoordSystem is now an array of struct pointers
modified GIFTI library, along with suma_gifti.c
08 May 2008, ZS Saad, 3dsvm, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed memory corruption caused by improper declaration of combName
08 May 2008, RW Cox, edt_dsetitems.c, level 1 (MICRO), type 0 (GENERAL)
new prefix *.hdr gets a 2-file NIfTI format output
08 May 2008, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Add 'u' or 'o' marker in titlebar to indicate what's the grayscale
08 May 2008, RW Cox, ROI drawing plugin, level 1 (MICRO), type 0 (GENERAL)
Change info label to show BRIK filename rather than dataset prefix
08 May 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
small changes to bilinear optimization parameters
08 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 5 (MODIFY)
updated help, NFIRST does not need to imply injection time
07 May 2008, RC Reynolds, make_random_timing.py, level 3 (MAJOR), type 1 (NEW_PROG)
generate random stimulus timing files
This generates random timing files suitable for use in 3dDeconvolve.
The timing is not restricted to a TR grid, though that is possible.
Consider use with '3dDeconvolve -nodata'.
07 May 2008, RC Reynolds, plug_3Ddump_V2, level 2 (MINOR), type 4 (BUG_FIX)
allow 4D datasets to be opened (so that buckets are again usable)
PLUGIN_dset_check() now checks NVALS instead of NUM_TIMES...
07 May 2008, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT)
added get_type_list and other accessor functions
02 May 2008, RW Cox, mcw_glob.c, level 1 (MICRO), type 0 (GENERAL)
added message from Graham Wideman when readdir() fails
01 May 2008, RW Cox, afni_cluster.c, level 1 (MICRO), type 0 (GENERAL)
Add SaveMask button to Clusterize report window.
Saves the clusters as a mask dataset (cluster #1 has value=1, etc.).
Uses the prefix in the text field for the dataset name -- will overwrite
existing dataset if the same name is used twice. Equivalent 3dclust
command is saved in History Note in output mask dataset (as if you had
pressed the '3dclust' button).
01 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
treat RESID_CT as Ct(t), not C(t)
30 Apr 2008, RW Cox, mcw_glob.c, level 2 (MINOR), type 3 (NEW_ENV)
setenv AFNI_SHELL_GLOB YES == wildcard expansion via the shell
For Graham Wideman and Mac OS X Server 10.5 problems.
30 Apr 2008, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 4 (BUG_FIX)
replaced make_stim_files with make_stim_times.py in help
24 Apr 2008, ZS Saad, SurfSmooth, level 1 (MICRO), type 4 (BUG_FIX)
Fixed leaky SurfSmooth.
Leak was from one of fin_float pointers in Head07
Also found leak in THD_extract_detrended_array and a few
more small leaks in other SUMA function. Valgrind is good.
23 Apr 2008, ZS Saad, afni-python, level 1 (MICRO), type 5 (MODIFY)
Changed methods in afni_name class
.path is now absolute
.inp() and .out() should be used to specify input and output volumes
Updated lpc_align.py and align_epi_anat.py to reflect changes.
17 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor changes
Child epi datasets can be volume registered even if parent epi
is a single sub-brick
16 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
multiple changes
Naming conventions for tlrc output, generic shell compatible,
regridding options for epi and tlrc epi output
14 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
minor change
3dAllineate options are also applied to epi to anat alignment,
so output EPI datasets get original resolution and type.
10 Apr 2008, RC Reynolds, afni_proc.py, level 1 (MICRO), type 0 (GENERAL)
updated the -help with information regarding runs of different lengths
10 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor changes
remove tabs in file, change output file names for epi children,
changes to help, and renamed tlrc parent option
08 Apr 2008, RW Cox, 3dUpsample, level 2 (MINOR), type 1 (NEW_PROG)
Upsample a 3D+time dataset (in the time direction)
08 Apr 2008, RW Cox, 3dTfitter, level 1 (MICRO), type 4 (BUG_FIX)
Deal with ref (LHS) vectors that are very tiny.
Modify thd_fitter.c so that ref vectors that are very tiny compared to
the largest one will not be included in the regression. Per the
unreasonable request of Rasmus Birn.
08 Apr 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 4 (BUG_FIX)
Weighting in LPC cost function
Realized that weighting in computing the LPC was only done on the blok
level computation of the PC. All the blok PC values were averaged
together without weighting. Modified code to use sum of weights over a
blok as a weight for its PC. This can be turned off by setting
environment variable AFNI_LPC_UNWTBLOK to YES (to restore the LPC
function to its previous behavior).
08 Apr 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 3 (NEW_ENV)
allow residual Ct values via AFNI_MODEL_D3_RESID_CT_DSET dataset
e.g. setenv AFNI_MODEL_D3_RESID_CT_DSET residual_Ct+orig
08 Apr 2008, RC Reynolds, 2dImReg, level 2 (MINOR), type 4 (BUG_FIX)
allow zero slices, passing input as result
Choleski factorization would fail on an empty slice. In this case,
return the input slices as the result (instead of crashing).
Done with D Glen.
08 Apr 2008, RC Reynolds, 3dNLfim, level 1 (MICRO), type 5 (MODIFY)
only update output every 100 voxels
07 Apr 2008, RW Cox, 1dUpsample, level 2 (MINOR), type 1 (NEW_PROG)
Upsample a 1D time series
07 Apr 2008, DR Glen, align_epi_anat.py, level 4 (SUPER), type 1 (NEW_PROG)
Alignment of EPI and Anatomical datasets
Aligns anat and EPI data. Alignment is in either direction of anat to
epi or epi to anat. Transformations are combined where possible as
from time series registration and talairach transformations. Multiple
child epi datasets may be aligned at the same time.
04 Apr 2008, RW Cox, 3dAllineate, level 2 (MINOR), type 0 (GENERAL)
Added '-nwarp bilinear' option
Experimental nonlinear warping comes to 3dAllineate at last.
Preliminary test looks good, but more work is needed to be sure it's OK.
04 Apr 2008, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL)
Check for ' ' option, which means a blank after a '\' character
02 Apr 2008, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Changed suma -environment's output to reflect user's current environment.
With this change, users can always replace their .sumarc with
the one output by suma -environment without worrying about loosing
their preferred settings.
02 Apr 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
extended maximum number of contrasts to 75
01 Apr 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
increased internal memory for 3dbucket and 3drefit command creation
31 Mar 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
extended maximum number of means, diffs and contrasts to 50
28 Mar 2008, RW Cox, 3dcalc, level 1 (MICRO), type 5 (MODIFY)
Treat auto-transposed .1D\' files as datasets, not as timeseries.
28 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -copy_gifti_meta and -copy_DA_meta options
28 Mar 2008, RC Reynolds, gifticlib, level 1 (MICRO), type 2 (NEW_OPT)
added routines to copy MetaData
28 Mar 2008, DR Glen, 3dDTeig, level 2 (MINOR), type 4 (BUG_FIX)
small negative eigenvalues are set to zero as in 3dDWItoDT
This fix avoids FA being set to 0 for those affected voxels
27 Mar 2008, ZS Saad, afni-matlab, level 2 (MINOR), type 5 (MODIFY)
Added other return options for Read_1D.m and BrikLoad.m
27 Mar 2008, ZS Saad, suma-general, level 1 (MICRO), type 5 (MODIFY)
Changed internal handling of various MATVEC sources.
Simplified handling of different sources of MATVECs from
AFNI's headers. Added handling of ALLINEATE_MATVEC to the
mix.
26 Mar 2008, ZS Saad, cat_matvec, level 2 (MINOR), type 5 (MODIFY)
cat_matvec can now output IJK_TO_CARD_DICOM and IJK_TO_DICOM_REAL
26 Mar 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -align_centers as an option to deal with very large moves
It used to be that users had to run @Align_Centers on all their
data when big moves were needed to align the surface's antaomy
to that of the experiment. This is no longer needed.
26 Mar 2008, ZS Saad, @Align_Centers, level 2 (MINOR), type 5 (MODIFY)
Script now outputs a matrix that represents the shift
This matrix can be used with 3dAllineate to perform the shift.
26 Mar 2008, ZS Saad, 3dvolreg, level 2 (MINOR), type 4 (BUG_FIX)
3dvolreg's -1Dmatrix_save was not always accounting for centers of rotation
Now the output of -1Dmatrix_save always matches what one would get for
the first sub-brick from
cat_matvec FRED+orig::VOLREG_MATVEC_000000 -I
26 Mar 2008, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
Add -norm2 and -normx options: normalize time series before plotting
26 Mar 2008, RC Reynolds, gifticlib, level 1 (MICRO), type 5 (MODIFY)
in compare, if comp_data is not set, state the fact
26 Mar 2008, DR Glen, python, level 2 (MINOR), type 4 (BUG_FIX)
repaired support for dry_run mode in python scripts
26 Mar 2008, DR Glen, matrix.c, level 1 (MICRO), type 4 (BUG_FIX)
freed matrix used in matrix_sqrt functions
25 Mar 2008, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Instead of SAME, one can use surface's name as LocalDomainParent
25 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
ROIs drawn on different surfaces now handled properly
25 Mar 2008, ZS Saad, ConvertSurface, level 1 (MICRO), type 2 (NEW_OPT)
Added option -ixmat_1D to apply inverse of affine transform
25 Mar 2008, ZS Saad, @auto_tlrc, level 1 (MICRO), type 5 (MODIFY)
Improvements on -rigid_equiv output and .1D transform output
25 Mar 2008, ZS Saad, @SUMA_AlignToExperiment, level 1 (MICRO), type 5 (MODIFY)
View is now changed even if rigid-body registration is used.
25 Mar 2008, RW Cox, 3dDetrend, level 2 (MINOR), type 4 (BUG_FIX)
-normalize didn't work -- what the hellll was I thinking?
Also, added some help to explain how to use 3dDetrend on 1D files.
25 Mar 2008, RW Cox, 1dnorm, level 2 (MINOR), type 4 (BUG_FIX)
Forgot the sqrt()! kudos to David Perlman.
25 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 5 (MODIFY)
the -compare_data option is not separate from -compare_gifti
25 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
minor changes:
- NIFTI_INTENT_NONE is considered valid
- added compare_gifti_data functions
- LabelTables are now written using CDATA
24 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 5 (MODIFY)
deconvolution with penalty factor = 0 is modified
Now the criterion for choosing the penalty factor is based on curvature
rather than distance from the origin. Seems to be more robust, but
probably will require yet more tweaking.
24 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added GERT_Reco options (request of D Glen)
-gert_filename : specify a name for the GERT_Reco script
-gert_nz : override nz=1 in mosaic image files
-gert_to3d_prefix : specify a dataset prefix for the to3d command
24 Mar 2008, RC Reynolds, @Align_Centers, level 2 (MINOR), type 4 (BUG_FIX)
applied proper follower dataset orientation and floating point shifts
The shift applied to the child datasets was based on the parent's
orientation. The shifts were also being truncated to integers.
Changed with D Glen.
21 Mar 2008, ZS Saad, 3dnvals, level 1 (MICRO), type 2 (NEW_OPT)
Added -all to 3dnvals to output all 4 dimensions.
21 Mar 2008, RW Cox, 3dTfitter, level 1 (MICRO), type 5 (MODIFY)
Modified operation of FALTUNG penalty=0 option
Implemented the L-curve method for selecting the penalty factor, when
user sets the factor to 0.
20 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
Add -polort option, to keep Gang Chen happy.
20 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_WRITE_1D_AS_PREFIX allows writing 1D or surface data given the prefix
For example, setting this to YES will allow writing surface data to NIfTI.
18 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -compare_gifti option
See 'gifti_tool -help' for details, including example #7.
18 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added comparison functions to gifticlib
17 Mar 2008, ZS Saad, lpc_align.py, level 1 (MICRO), type 2 (NEW_OPT)
Added -big_move and -partial_coverage.
-big_move is for when large displacements are needed for alignment.
-partial_coverage is for when EPI covers a portion of the brain.
17 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if 1 volume, GERT_Reco_dicom does not give (useless) timing to to3d
14 Mar 2008, RW Cox, 3dROIstats, level 1 (MICRO), type 2 (NEW_OPT)
Sub-brick label printing (and -nobriklab option)
Per the noble Vince Hradil.
13 Mar 2008, RC Reynolds, 3dmerge, level 2 (MINOR), type 0 (GENERAL)
added some examples to the -help output
12 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Changed surface controller font to 8.
You can get the old font size with environment
variable SUMA_SurfContFontSize BIG.
The default is now SMALL.
12 Mar 2008, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Changed crash in SurfaceMetrics when -spec and -i options are mixed.
11 Mar 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 2 (NEW_OPT)
added control of hematocrit via AFNI_MODEL_D3_HCT
10 Mar 2008, RC Reynolds, SUMA_SurfMeasures, level 3 (MAJOR), type 4 (BUG_FIX)
averages did not include nodes lost to -cmask
Noticed by M Beauchamp.
10 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_GIFTI_VERB sets the verbose level in the gifti I/O library
The default is 1, 0 is quiet, and values go up to 7.
10 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 0 (GENERAL)
AFNI can read/write .gii.dset as with .gii
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
applied -gert_outdir in the case of dicom images
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if only 1 run, GERT_Reco_dicom is named per run
07 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Color map in surface controller can be flipped and rotated
* f key for flipping colormap
* Up/Down keys for rotating color map
* Home for home
Hit ctrl+h on Surface Controller's colormap for more help.
07 Mar 2008, RW Cox, Dataset#N, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_DATASETN_NMAX sets number of datasets allowed
New environment variable AFNI_DATASETN_NMAX sets the number of datasets
allowed in Dataset#N plugin, from 9..49. This is for Shruti.
07 Mar 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 4 (BUG_FIX)
properly ignore empty lines, and exit on short files
06 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Added three variables affecting the surface controller
* SUMA_ShowOneOnly: Sets '1 Only' on or off. On by default
* SUMA_GraphHidden: Update open graphs even if corresponding dset
is hidden.* SUMA_ColorMapRotationFraction: Fraction of
colormap to rotate
up or down with arrow keys.
See suma -environment for a complete list.
06 Mar 2008, RW Cox, 3dcalc, level 1 (MICRO), type 5 (MODIFY)
Add cbrt (cube root) function to parser; affects 1deval and ccalc
06 Mar 2008, RC Reynolds, GIFTI, level 1 (MICRO), type 5 (MODIFY)
allow functional control over GIFTI encoding
05 Mar 2008, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
Support for GIFTI surface format writing
GIFTI writing can now be done with SUMA programs.
For example, see options -o_gii and -xml* in ConvertSurface program.
05 Mar 2008, RW Cox, afni-general, level 2 (MINOR), type 5 (MODIFY)
Change the way 1D datasets are written to disk from 3D programs
In programs that analyze time series files (such as 3dTfitter), you can
input 1D files and make the column direction be the time axis by using
suffixing the file with \' -- but when it comes to writing the results
dataset out, the standard AFNI I/O method is to write the time axis
along the row direction. With this change, if you input a 1D file in
the place of a 3D dataset AND put '.1D' at the end of the output file
prefix, then the output dataset will be written so that the time axis
is along the column direction.
05 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
added '-fitts' option to produce fitted time series dataset
05 Mar 2008, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Added 'AFNI History' button to the Datamode->Misc menu
05 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixed passing of INDEX_LIST
05 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
do not duplicate data when reading and writing GIFTI from AFNI
04 Mar 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
couple of small changes to help the hapless users
* add more informative error message if allocate_memory() fails
* force '-float' if any output prefix is NIfTI-1 format (.nii)
04 Mar 2008, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
added -accumulate option, to output each partial sum
for k = 0..N-1 : output[k] = sum(input[i]) over i = 0..k
03 Mar 2008, RW Cox, ++AFNI_History++ plugin, level 1 (MICRO), type 2 (NEW_OPT)
Small changes to make onscreen wordwrap match printout wordwrap
03 Mar 2008, RC Reynolds, website, level 2 (MINOR), type 5 (MODIFY)
updated the AFNI History website pages, with a table of entries
01 Mar 2008, RW Cox, ++AFNI_History++ plugin, level 1 (MICRO), type 1 (NEW_PROG)
Provides a way to create and insert entries into afni_history_NAME.c
User must set two environment variables:
AFNI_HISTORY_PERSONAL_FILE = full path to your personal version of
afni_history_NAME.c
AFNI_HISTORY_USERNAME = what you want for the username in your file
My values of these are
AFNI_HISTORY_PERSONAL_FILE = /Users/rwcox/AFNI/src/afni_history_rwcox.c
AFNI_HISTORY_USERNAME = RWC
You also need to add one of two lines to your afni_history_NAME.c file:
/*=====below THIS LINE=====*/
or
/*=====above THIS LINE=====*/
as shown, with no blanks before or after on the same line (except that
you must make 'BELOW' or 'ABOVE' all caps!).
New history entries are placed below the 'BELOW' line (if present), or
above the 'ABOVE' line.
If you set AFNI_HISTORY_DONTSAVE to YES, then the afni_history_NAME.c
file won't be edited, and the new entry is just written to stdout.
29 Feb 2008, RW Cox, afni_history, level 1 (MICRO), type 0 (GENERAL)
with HTML output, put a rule between different dates
29 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added a TYPE, -type, a new level, and a string to identify each level
29 Feb 2008, G Chen, 3dICA.R, level 4 (SUPER), type 1 (NEW_PROG)
Independent component analysis
This is an R program that runs independent component analysis. It
takes one dataset that presumably has already been properly
pre-processed.already been properly pre-processed. See more details at
http://afni.nimh.nih.gov/sscc/gangc/ica.html
28 Feb 2008, ZS Saad, suma-general, level 3 (MAJOR), type 3 (NEW_ENV)
Support for GIFTI surface format reading
28 Feb 2008, RW Cox, 3dUndump, level 2 (MINOR), type 0 (GENERAL)
allow input of NO text files, to produce an 'empty' dataset
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow constraints on sign of deconvolved function
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow combination of penalty functions in deconvolution
28 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -list_authors option and adjusted spacing
27 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Addition of p and q values under threshold bar
Use BHelp on p and q text in suma to get more info.
27 Feb 2008, ZS Saad, suma-general, level 1 (MICRO), type 4 (BUG_FIX)
Another bout of initialization and leak fixes based on valgrind's output
The hope is that some weird X behavior is caused by uninitialized
variables.
27 Feb 2008, RW Cox, 3dTfitter, level 3 (MAJOR), type 2 (NEW_OPT)
add deconvolution via the '-FALTUNG' option
Unlike 3dDeconvolve, this deconvolution is to find the input time
series, given the impulse response function.
27 Feb 2008, RC Reynolds, afni_history, level 4 (SUPER), type 1 (NEW_PROG)
program to display the history of AFNI updates
This will be used to create a web page of AFNI updates.
Please see 'afni_history -help' for more details.
27 Feb 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed -regress_use_stim_files typo (was -regress_use_stim_times)
26 Feb 2008, RC Reynolds, afni_history, level 1 (MICRO), type 0 (GENERAL)
checked in initial afni_history files
25 Feb 2008, RW Cox, 1dsvd, level 2 (MINOR), type 2 (NEW_OPT)
add '-vmean' and '-vnorm' options, to mirror capabilities in 3dpc
25 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Make 3dTfitter work when -RHS is a '1D:' input (-LHS already worked).
* -vnorm and -vmean options for 1dsvd.c (as in 3dpc.c).
25 Feb 2008, RC Reynolds, plug_vol2surf, level 3 (MAJOR), type 4 (BUG_FIX)
fixed application of cluster for sending data to suma
Previously, clustering was only applied when the Olay and Thr sub-bricks
were the same.
24 Feb 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
GIFTI library now considers MetaData without Value as valid
22 Feb 2008, RW Cox, 3dpc, level 2 (MINOR), type 2 (NEW_OPT)
add '-eigonly' and '-reduce' options; output eigenvalues to a 1D file
'-eigonly' causes 3dpc to print eigenvalues to stdout and stop there.
'-reduce n pp' outputs a reduced dataset, using only the largest 'n'
eigenvalues.
22 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to 3dpc.c: -reduce and -eigonly options.
21 Feb 2008, RC Reynolds, GIFTI, level 4 (SUPER), type 0 (GENERAL)
AFNI programs can now read and write GIFTI datasets
GIFTI datasets are for data in the surface domain, with file suffix .gii.
Support must be requested at compile time, and it requires libexpat.
Please see http://www.nitrc.org/projects/gifti for many details.
20 Feb 2008, RW Cox, 1deval, level 2 (MINOR), type 2 (NEW_OPT)
add '-1D:' option, to write output that is usable on the command line
Sample usage:
1dplot `1deval -1D: -num 71 -expr 'cos(t/2)*exp(-t/19)'`
The backquotes `...` capture command's output and put this string on
the command line. The '-1D:' option formats the 1deval output so that
it is ready to be used in this way.
20 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add cl2.c constrained least squares function to the library.
* Use this in thd_fitter.c and thence in 3dTfitter.c.
* Add '-1D:' option to 1deval.c.
19 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Bug fixes in 3dTfitter.c and thd_fitter.c.
16 Feb 2008, RW Cox, 3dTfitter, level 4 (SUPER), type 1 (NEW_PROG)
new program = linear fits to voxel time series
Uses L1 or L2 regression, with optional constraints to fit each voxel
time series as a sum of basis time series, which can be 1D files or
3D+time datasets. Basis time series that are 1D time series are
the same for all input voxels. Basis time series that are 3D+time
datasets are different for each voxel.
Differences from 3dDeconvolve:
* Basis time series can vary across voxels.
* Fit coefficients can be found with L1 or L2 error functions, and
can be constrained to be positive or negative.
* 3dTfitter does not compute goodness-of-fit statistics.
16 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program 3dTfitter. And fitting function THD_fitter().
14 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Graphing of dset content with 'g'
A graph of the column content at a node can be plotted
This would be the surface equivalent to AFNI's graphing function.
See suma's interactive help 'ctrl+h' for more info.
14 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Similar changes to de-clusterize when a forced view switch occurs when
switching datasets, or when switching datasets to something that
doesn't have data available.
* Also, AFNI_FLASH_VIEWSWITCH to disable Adam Thomas's view switching
flashiness.
13 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify mcw_glob.c and thd_mastery.c to pre-expand '~/' at the start of
a filename to '${HOME}/' to help some pitiful users (e.g., me).
* Modify afni.c to turn off clusterizing when switching coordinate systems
.
12 Feb 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
An option to show all of suma's environment variables
See help for -environment in suma -help.
11 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c and thd_mastery.c to work better with '3dcalc' command
line datasets.
07 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* DSET_overwrite() macro, and THD_force_ok_overwrite() function.
* Modify plug_drawdset.c to use DSET_overwrite(), and a few other
plugins and 3d*.c programs as well.
* Fix drawing of surface overlay when the functional overlay is being
shown as the underlay: must use the underlay dataset for coordinate
checking even if overlay dataset is actually being drawn as underlay,
since the coordinates for the images are still the underlay's in
this situation.
* Fix 3dvolreg to work properly with sub-brick scale factors.
06 Feb 2008, ZS Saad, SurfDist, level 3 (MAJOR), type 1 (NEW_PROG)
Program to calculate geodesic internodal distances
06 Feb 2008, RC Reynolds, 3dbucket, level 2 (MINOR), type 0 (GENERAL)
modified to copy FDR curves
05 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fix over-write checks in mri_write.c by moving all file open/close
operations to new fopen_maybe() and fclose_maybe() functions.
* Move THD_deathcon() and THD_ok_overwrite() functions to afni_environ.c,
where they belong.
* New function EDIT_geometry_constructor() to make an empty dataset from
a string specifying it's geometry. Also, print this geometry string
in 3dinfo.
04 Feb 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_NEWSESSION_SWITCH in afni_func.c == switch to new session?
01 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* VOLUME_DATA_SPARSE in thd_nimlatr.c.
* READ_NIML_FILE in afni_driver.c.
* Force re-clustering when doing a redraw in the ROI plugin.
* Modify NIML+PO button label to reflect status of NIML and plugouts
at time button is created.
31 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify plug_crender.c to obey AFNI_SLAVE_THRTIME.
29 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Fixed bug in 3dFDR -new handling of mask -- ooooppssssie.
* And bug in FDR curves generated from signed statistics (like t).
28 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Added PRINT_COMPILE_DATE macro to mrilib.h and to a lot of programs'
-help output.
* Fixed 'rule of 15' bug in afni_cluster.c, where the initial display only
showed a max of 15 widget rows, even if there were more clusters, but
the number of rows would be reset correctly on any re-clusterizing.
Problem: didn't initialize maxclu_default at the right location.
* Fixed problem with display of clusterized dataset which is both the
Underlay and Overlay: the Underlay was being shown as the edited
volume, but that looks real bad. Solution: disable vedit feature
in AFNI_dataset_slice() when calling from the 'get anat image' place
in afni.c, and then re-enable it right afterwards.
25 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* mri_read_1D_stdin() in mri_read.c.
24 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add FDR curve generation to 3dANOVA.lib, 3dNLfim, 3dRegana, 3dttest.
* Fix little problems with AFNI threshold scale display as q-value alters.
* Fix bug in thd_mastery.c in assiging FDR curves to mastered sub-bricks.
* Add '-killSTAT' option to 3drefit.
23 Jan 2008, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* FDR thresh-vs-z(q) curve generation and storage in datasets.
* Display FDR q in AFNI pval label.
* Generate FDR curves automatically in 3dDeconvolve, and with
'-addFDR' option in 3drefit.
22 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Minor changes to 3dFDR: better help, -float, -qval.
* Add -sort and -SORT options to 3dcalc, for no good reason.
* Add 'help' command to ccalc, to give parser info.
22 Jan 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options to estimate smoothness in data for use in AlphaSim
See help options -regress_est_blur_epits and -regress_est_blur_errts.
18 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Incorporate mri_fdrize() into 3dFDR.
17 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* AFNI_FLOATIZE environment variable for 3dDeconvolve.c and 3dcalc.c.
* mri_fdrize.c function for FDR-z conversion.
16 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Fix clusterize so that too small a value of vmul means just set the
min cluster volume to 2 voxels.
* Unfixed bug: display of clusterized func+tlrc.BRIK when func+tlrc datase
t
is warped from func+orig -- must fix afni_warp.c in this case.
12 Jan 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Scroll lists for I T and B selectors in suma
Right click on pulldown menu titles to get
a scroll list instead. This makes selecting from
a long list of options, or columns, much easier.
Right click on 'I' to the left of suma's Intensity Selection
button for an illustration.
11 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Small changes to AlphaSim.c, like using -fast option and better help.
* Scrolling window changes to afni_cluster.c (Clusterize report panel).
* mri_alphasim.c seems to work now.
09 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* SIGQUIT delay in afni.c, for Jerzy.
28 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Popup menu in clusterize report to set histogram range.
28 Dec 2007, RC Reynolds, gifti_tool, level 3 (MAJOR), type 1 (NEW_PROG)
program to read and write GIFTI datasets
27 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Upgrades to clusterize reporting window: histograms, from/to indexes
on auxiliary dataset, 3dclust and save table buttons, &c.
* Fixed bug in DG's obliquity reporting function in thd_coords.c -- it
didn't check if the input dataset was valid -- caused AFNI to crash.
20 Dec 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* Clusterize reporting window.
19 Dec 2007, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
Use of '[i]' to select node index from surface dset
Square bracket '[]' selection works for surface-based
datasets much like it does for volume-based ones.
In addition, one can use '[i]' to select the indices
of nodes for which data are defined in a particular
surface-based dataset.
For more information, see 'SUMA dataset input options:'
section in the output of ConvertDset -help .
18 Dec 2007, ZS Saad, ROIgrow, level 2 (MINOR), type 1 (NEW_PROG)
Grows regions separately, depending on labels
18 Dec 2007, ZS Saad, ROI2dataset, level 2 (MINOR), type 0 (GENERAL)
Output full datasets if needed
17 Dec 2007, ZS Saad, ConvertDset, level 2 (MINOR), type 0 (GENERAL)
Output of full dsets if needed
This can be used to force a dataset with data
defined on a few nodes to be written out with a
complete list of nodes, using 0 where no data are defined.
06 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add -jpg and -png options to 1dplot.c.
* Add thick line drawing to mri_coxplot.c (by repeated thin line drawing).
05 Dec 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify plot_motif.c to allow saving plots (as in 1dplot.c) to .jpg and
.png files (if the proper suffix is given).
04 Dec 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add AFNI_driver_register() to afni_driver.c to allow a plugin (say) to
register a driver callback function.
03 Dec 2007, RC Reynolds, GIFTI, level 3 (MAJOR), type 0 (GENERAL)
initial release of gifti I/O C API
23 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 1 (NEW_PROG)
Older History stuff
* Modify NI_decode_one_string() in niml_elemio.c to auto-expand buffer
size if string is too long. For festering Lebanese programmers.
* Similarly, modify scan_for_angles() if element header is bigger than
buffer size.
* 'Histogram: Multi' (plug_histog_multi.c) plugin, for Kyle, Alex, & Pat.
20 Nov 2007, RW Cox, 3dTsort, level 3 (MAJOR), type 1 (NEW_PROG)
new program = sorts voxel data along the time axis
This might be useful for sorting the -stim_time_IM beta weights
output be 3dDeconvolve. Perhaps for something else, too?
20 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 1 (NEW_PROG)
Older History stuff
* Copy auxdata from source to output in 3dAllineate.c (oops).
* Changed 'report' from mri_clusterize.c and added info to the
clusterize vector chooser using about BHelp to see this report.
* New program 3dTsort.c. Will this grow to be a monster?
19 Nov 2007, ZS Saad, Surf2VolCoord, level 2 (MINOR), type 1 (NEW_PROG)
Program to show surface-node to voxel correspondence
This can be used to understand how surface coordinates
relate to voxel coordinates.
16 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Added -global_times, -local_times, and -guess_times to 3dDeconvolve.c
* For ragged 1D input files, arbitrary text starting with alphabetic
character is same as '*' for filler.
* AFNI_RESCAN_AT_SWITCH is on by default now.
* 1dplot takes a 1 row file and flips it to a column for plotting; however
,
when 2 single row files were input, they'd be catenated and THEN
flipped, producing erroneous joined plot. Now, they are flipped
THEN catenated, which does the right thing.
* Speaking of 1dplot, '-nopush' now works for multiple graphs, rather
than just for '-one'.
* Modify AlphaSim.c so that rmm defaults to -1 ==> nearest neighbors,
and so that '-seed 0' generates a custom seed.
* Add some extra text to the 'Clusterize' label (afni_setup.c) to
explain that rmm=0 means NN clustering with vmul in voxel count.
15 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to interactive AFNI to save '1D:' ref and ort files in the
header of interactive fim files; example
1dplot '`3dAttribute -ssep ' ' AFNI_FIM_REF r1_time@1+orig`'
* Changes to mri_read_1D() to allow arbitrarily long filenames.
* New function mri_to1Dstring(), to create '1D:' strings from MRI_IMAGEs.
13 Nov 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* SAVE_RAW and SAVE_RAWMONT commands in afni_driver.c (and so imseq.[ch]).
* Fix error in mri_genalign.c for allcost: the various 'cr?' functions
weren't being properly separated.
* Added multiple -check ability to 3dAllineate.c, and -allcost now printed
for each alternative checked parameter set as well.
09 Nov 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in build_2Dhist() in thd_correlate.c equal sized bin code,
where 'ytop-xbot' was used instead of 'ytop-ybot'. This is obviously
the work of Dutch saboteurs.
05 Nov 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Insert some sleeping to try to avoid X11 errors that have been reported
(but not seen by me) about XGeometry.
* If DONT_USE_XTDESTROY is #define-d, then XtDestroyWidget() is replaced b
y
XtUnrealizeWidget() -- this is used in the Makefile for linux_xorg7,
where the old bug in that Xt library function seems to have risen
from the dead.
29 Oct 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Change 'workmem' default to 266 in several of Doug Ward's programs.
* Added warning message to 3dDeconvolve if TENT() or CSPLIN() inter-knot
TR is smaller than the output TR for -iresp.
* Added message to 3dSynthesize.c to indicate type of -cenfill being done.
26 Oct 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified ranks.c and 3dMannWhitney.c to create sorted list all at once
(via qsort_float), hopefully speeding things up. Also increased
default workmem and MAX_OBSERVATIONS.
* Same deal for 3dWilcoxon.c.
25 Oct 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Minor change to RegAna.c to use matrix_psinv() as a backup to
matrix_inverse_dsc() when inverting GLT matrix.
24 Oct 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Minor fix to 3dAllineate.c to setup 'blok' stuff when allcost is on.
16 Oct 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Small bug in decode_linebuf() in mri_read.c -- if a non-number character
is encountered in non-slowmo mode, infinite loop ensues and that's bad.
Now, such an encounter leads to an immediate break out of the loop.
* Small changes to approximate_number_string() and it's usage in 3dDeconvo
lve.
* Fix to afni_graph.c so that 'Boxes' plot mode turns off 'Double Plot'.
12 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Changes to bbox.c to add an arrowval index selector to the single-select
ion
mode strlist chooser (per Shruti Japee's unreasonable demand).
11 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify edt_filtervol.c to clip off voxels outside the fmask.
* Modify 3dmerge.c to add -1fm_noclip and -1filter_blur options.
10 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to 3dDeconvolve.c to check -stim_label values: for un-assigned
values, and for duplicate values.
* Change a few programs to check EQUIV_GRIDS() as well as voxel counts,
when combining multiple datasets (3dTcat, etc).
* Modify plug_nth_dataset.c to use different set of default overlay colors
.
Modify afni_plugin.[ch] to allow this.
* Modify afni_graph.c to make 'Transform 1D' menu re-activate a button eve
n
if it is already the activated one. Goal: popup Dataset#N plugin
controls more easily.
* Modify 3dttest.c to add the -sdn1 option (for Tom Johnstone).
04 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify afni_graph.c to turn Double Plot on when Dataset#N is invoked,
and to not double plot transformed time series that didn't change.
* Print 'NFirst > 0' informational message in 3dDeconvolve.c.
* Change OPACITY_BOT from 0 to 1 in imseq.c.
26 Sep 2007, ZS Saad, SurfFWHM, level 4 (SUPER), type 1 (NEW_PROG)
Program to estimate FWHM of data on surface
26 Sep 2007, ZS Saad, SurfSmooth, level 3 (MAJOR), type 5 (MODIFY)
Big changes to data smoothing functions
* HEAT_07 method does controlled blurring, with options
to blur 'to' a particular FWHM. No guessing needed for
iterative kernel bandwidth or number of iterations.
* HEAT_05 method improved to reduce numerical precision
problems.
21 Sep 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified MCW_choose_vector() in bbox.c to make initvec a float array,
and then fixed the clusterize and graph pin stuff to match.
* Modified thd_info.c to print out a more prominent warning message
from 3dinfo.c when sub-brick stats are hidden from the user.
* Warning message popup when Define Markers is first opened on a
marker-less dataset.
20 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add '-allcost' options to 3dAllineate.c and mri_genalign.c.
* Neuter program 3dAcost.c.
* Environment variable AFNI_INDEX_SCROLLREV.
20 Sep 2007, G Chen, 3dLME.R, level 4 (SUPER), type 1 (NEW_PROG)
An R program for linear mixed-effects analysis at group level in AFNI
See more details at http://afni.nimh.nih.gov/sscc/gangc/lme.html
18 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'RGB:r,g,b' format to DC_parse_color() in display.c.
* Fixed some bugs in 'Clipped' display.
17 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'Clipped' option to image grayscaling, in imseq.c and afni.c.
12 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'All AFNI Splashes' button to 'hidden' menu, just for fun.
11 Sep 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Modified 3dBlurToFWHM.c to remove scale factors from 'outset' if 'inset'
had them. Oopsie.
10 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Minor changes to 3dAllineate.c: '-autoweight**1.5' sub-option;
'-autoweight' now the default for '-ls' cost function.
* Re-insert older fixes to afni.c that were lost in CVS.
31 Aug 2007, RC Reynolds, DECONFLICT, level 3 (MAJOR), type 5 (MODIFY)
modified default behavior of programs from deconflict to no overwrite
See AFNI_DECONFLICT in README.environment.
31 Aug 2007, RC Reynolds, model_conv_diffgamma, level 2 (MINOR), type 1 (NEW_PROG)
NLfim model to compute the convolution of the difference of gammas
20 Aug 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* First version of '-lpc' Local Pearson Correlation cost function in
3dAllineate.c, with rhombic dodecahedra as the default building bloks.
16 Aug 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Modify 3dDeconvolve.c to check -stim_times files for 0-1 inputs and for
duplicate times.
14 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify 3dDeconvolve.c to allow 'POLY' model to have order up to 20.
* Modify 3dLocalBistat.c to allow '-weight' option for '-pearson' statisti
c.
08 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add threshold signage feature to AFNI threshold menu ('Pos & Neg', etc).
03 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_SEE_OVERLAY environment variable.
* Turn overlay on when user first-time switches Overlay, and turn TTatlas
colors on when user pops up atlas color chooser panel.
01 Aug 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify to3d.c to warn users of '-xFOV 120A-P' (e.g.) that this is a 240
mm
field of view (warn in the -help output, and in the program running).
31 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Make -cmass the default in 3dAllineate.c.
* Also add '+clip' feature to '-autoweight' in 3dAllineate.c.
30 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify thd_read_vecmat.c to use mri_read_double_ascii() to read a file r
ather
than read it directly. This way, comments will be skipped properly and
the '1D: ...' format can be used.
* Fix afni_plugin.c to initialize loading of matrix_initialize(), to fix a
problem left in plug_deconvolve.c by RCR's matrix.c changes.
* Matrix square root in mri_matrix.c, and thence to 1dmatcalc and cat_matv
ec.
30 Jul 2007, RC Reynolds, regression_tests, level 3 (MAJOR), type 0 (GENERAL)
added setup for regression testing to NIFTI package
This can be used as a template for testing any command-line programs.
27 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add 'SPMG3' to 3dDeconvolve.c.
* Fix bug in -1Dmatrix_save in 3dAllineate, when dealing with zero-padded
base.
25 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dAllineate, 3dvolreg, and 3dWarpDrive to output base-to-source m
atrices.
* Modify cat_matvec to deal with files of multiple matrices.
* Modify 3dAllineate to make '-clbin 0' the default.
* Modify afni to add an AutoThreshold button to the threshold popup menu.
19 Jul 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add THD_multiplex_dataset() to thd_mastery.c, and thence 3dttest.c.
* Modify 3dAllineate to re-use last row of -1Dapply input if needed, and
also to print a warning that -master may be needed with -1Dapply.
16 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -stim_times_IM to 3dDeconvolve.c, to get individual event amplitudes
.
11 Jul 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Minor tweaks to algorithm for setting voxel-dependent blur factors in
3dBlurToFWHM.c.
* Various #define's for SOLARIS bad functions like fabsf() in 64 bit mode.
29 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Boxed plots work with Dataset#N now, in glorious colors and thinned.
But not with Double Plot.
28 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Threshold on/off in reactivated thr_label popup menu in Define Overlay.
* -x1D_stop in 3dDeconvolve.
26 Jun 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* Boxed plots in afni_graph.[ch]. Probably a can of worms.
25 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to 3dDeconvolve and 3dSynthesize so that censored time points
can be reconstructed in some fashion in the latter program.
* -x1D_uncensored in 3dDeconvolve.
06 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify thd_writedset.c to always do THD_deconflict_prefix(), unless told
not to by AFNI_DONT_DECONFLICT. Modify a bunch of 3d programs to NOT
check for filename conflict on output.
* Modify thd_correlate.c build_2Dhist() to avoid histogram overflow (oops)
.
05 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dBlurToFWHM.c and 3dFWHMx.c to use detrending.
* Add THD_patch_dxyz_* functions to thd_auxdata.c, to make sure MRI_IMAGE'
s
in a dataset have the correct dx,dy,dz fields.
04 Jun 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify 3dDeconvolve.c to use .xmat.1D instead of .x1D as output filename
for matrices.
01 Jun 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifiy mri_dicom_hdr.c to use a larger buffer for RWC_printf() function
,
which may help with really big DICOM header files.
30 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dDeconvolve mmap() usage to include MAP_NORESERVE flag.
* Add -allzero_OK option to 3dDeconvolve.c.
* Make 3dttest check for duplicate dataset filenames.
29 May 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Enforce RadioAlwaysOne behaviour on marks toggles.
* Modify 3dDeconvolve to do proper kill-off of children when fork() fails.
* Fix SPMG model power from 4 to 5.
* Modify symeigval_double() to report nonzero error code from rs_().
10 May 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* -izz option to 3dAllineate.
* L1 detrending in thd_detrend.c (and retrending).
09 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New advanced histogram options '-clbin' and '-eqbin' for 3dAllineate.
04 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* 'amongst' function in parser.f and so in 3dcalc.c.
* Added more warnings to 3dDeconvolve.c, including a parametrized -GOFORIT
.
03 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'crop=' to afni_driver.c image window opening, and also to afni_sp
lash.c
when saving .afni.startup_script file. [Per John Butman]
* Modified 3dDeconvolve.c to print clearer messages when -gltsym errors
occur, and also to allow the Decon -bucket dataset to be overwritten,
and also to add the -nobucket option. [Per Mike Beauchamp]
30 Apr 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Included 3dinfo.c patch from Colm Connolly with -label2index option.
27 Apr 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_niftiread.c to always do floatscan on datasets.
* Modified 3dDeconvolve.c to make 0.0 ABI paired values not require -GOFOR
IT.
26 Apr 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify imseq.[ch], afni.c, and afni_graph.c to use '[' and ']' keys for
time index incrementing, per John Butman.
04 Apr 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dDespike.c to add -localedit option.
* Modify 3dAllineate.c to save matrices into header of output.
03 Apr 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify edt_blur.c to compute FIR Gaussian weights as a local sum across
each cell, rather than just the weight at the center of the cell.
27 Mar 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Help for cluster editing, and some rationalization (e.g., reset it when
changing datasets, turn widgets off if it's not avaiable, et cetera).
26 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Moved on-the-fly cluster editing to Define Overlay panel, from popup men
u.
23 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New function THD_deconflict_prefix() in thd_opendset.c.
* Modify 3dDeconvolve.c to deconflict output prefixes (instead of failing)
,
and to compute Full F by default, unless -nofullf_atall is given.
* AFNI_IMAGRA_CLOSER, for the FC5 abusers out there.
22 Mar 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Make THD_filesize() return a 'long long', and change mri_read_3D() to
match. (This is Colm Connolly's fault.)
21 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New program 3dEmpty.c.
* Fix 3dinfo.c to allow empty datasets (duh).
20 Mar 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* MCW_discard_events_all() in xutil.c, and its application to stop
over-scrolling in imseq.c, et cetera.
* -nox1D in 3dDeconvolve.c.
* Make -bout be always on for 3dDeconvolve -input1D.
16 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* -polort A and polort degree warning message.
* Change CTENT() to CSPLIN().
15 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added CTENT() to 3dDeconvolve.c, for experimental purposes.
* Modified bucket labels in 3dDeconvolve.c to be clearer (to me, anyhoo).
14 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New program 1dMarry.c.
13 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Minor changes to 3dSynthesize.
* Change PRINT_VERSION() macro in mrilib.h to include compilation __DATE__
in output.
* '-float' option to 3dDeconvolve. Also a few little other fixes.
12 Mar 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* New program 3dSynthesize.c.
10 Mar 2007, ZS Saad, MapIcosahedron, level 2 (MINOR), type 5 (MODIFY)
Better handling of surface centers
09 Mar 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* First test of -stim_times_AM? looks good.
* MCW_discard_events() for Button4/5 ScrollWheel actions.
08 Mar 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add mri_read_ascii_ragged_complex() to mri_read.c.
* And modify mri_write_ascii() in mri_write.c to write complex numbers
with ';' as a real/imag separator, instead of ' '.
07 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* 3dDeconvolve.c: -GOFORIT, check_matrix_condition(), report -stim_times
values outside of run intervals, condition numbers with and without
baseline regressors.
06 Mar 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed pairmin() bug in parser.f.
* Store column_metadata in 3dDeconvolve.c, and write it to -x1D file
if AFNI_3dDeconvolve_NIML is YES.
05 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -nfft and -detrend options to 3dDFT.
* Added 'u' and 'o' image viewer keypress handling to afni.c.
* Added Mod+Button4+5 threshold slider changing to imseq.c and afni.c.
* Added AFNI_THRESH_AUTO to afni_func.c.
04 Mar 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed overrun bug in THD_extract_array() for raw data -- code was never
tested! Affected 3dDFT.c.
02 Mar 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified -CENSOR to -CENSORTR (for Rick's sake) and added '*' capability
to the run syntax.
* Added 3dDFT.c, from Kevin Murphy.
01 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add dilation to -automask option in 3dAllineate. And -ignout option.
* Add -CENSOR to 3dDeconvolve.c.
27 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_DISABLE_TEAROFF environment variable.
26 Feb 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to make the Session selection dialog directory-
specific, and the 1D selection dialog regular-file-specific. Also
changed the labels on top of the file list for each case.
* Modified xutil.c so that MCW_expose_widget() doesn't do anything for
a non-widget (e.g., gadget) input.
* Added Ziad's Xt translations for Button4 and Button5 scrolling.
* Fixed mri_medianfilter.c: had logic for usedxyz exactly backwards! Oopsi
e.
* Added Button4+5 image window scrolling to imseq.c, and to afni_graph.c
* If only dummy dataset is present, then 'Switch Session' opens up the
'Read Session' dialog.
23 Feb 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Change XmNtraversalOn from False to True in about 1 zillion places, to
make keyboard focus be kept better in text widgets.
* Added 'dset=NULL' initializer to THD_open_one_dataset() in thd_opendset.
c,
per Bernd Feige of Freiburg.
* Modified bbox.c to make AFNI_list_doubleclick default be 'Apply' rather
than 'Set'.
* Modified afni_func.c to replace 'RescanTh' button with 'EditEnv' if
Ziad's AFNI_RESCAN_AT_SWITCH is turned on.
* Modified afni_func.c to do AFNI_RESCAN_AT_SWITCH only for 'Overlay'
and 'Underlay' buttons. (It's pointless for 'Switch Session'.)
22 Feb 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_loaddblk.c to do floatscan on ANALYZE (etc.) datasets.
* Also modified thd_floatscan.c to add functions to scan MRI_IMAGEs
and other AFNI-ish assemblies of numbers.
* Modified afni.c to parse multiple commands in a single '-com' option,
separated by ';' (or by the choice in '-comsep').
* Modified afni_driver.c to allow use of 'axial_image' (etc.) as easy
typos for 'axialimage' (etc.).
* Modified dist_help script to include README.* files.
21 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified Edit Environment pseudo-plugin (afni_pplug_env.c) to sort
controls by variable name.
* Added 'instant switch on selection' mode to 'Overlay' and 'Underlay'
dataset choosers, controlled by AFNI_DATASET_BROWSE variable.
* And to 'Talairach To' controls.
* Fixed bug when '-R' would fail to find any datasets, and would then
try to reconcile parents, look for duplicates, etc., de-referencing
NULL pointers. Not sure what happened, actually, but one technique
was to avoid trying to read directories as regular file datasets.
20 Feb 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify list choosers in bbox.c to add XmNtraversal = True, so that arrow
keys can be used to move around in lists.
* Also add TEAROFFIZE() macro to xutil.h and use it to make most popup or
pulldown menus in AFNI have the 'tear off' feature.
* When Datamode->Misc->Purge Memory is used, and mcw_malloc() is turned on
,
prints out the before and after usage, just for fun.
18 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* When running 'afni' (no directory args) and no data is found is './',
then afni.c will now recurse 1 level on './' to see if any datasets
can be found 1 level deeper. Inspired by Korea workshop and Hame Park.
15 Feb 2007, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
High resolution image saving with ctrl+r
Very high resolution images can be created.
See suma's interactive help 'ctrl+h' for more info.
05 Feb 2007, ZS Saad, SurfDsetInfo, level 2 (MINOR), type 1 (NEW_PROG)
Program to display surface dataset information
Output is crude at the moment.
05 Feb 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add AFNI_OVERLAY_ONTOP environment variable, to move 'Overlay' button
above 'Underlay'. Also, change bg of 'Underlay' to black, to
distinguish it better from 'Overlay'.
02 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added a 'Rescan' button next to 'Overlay' and 'Underlay' in the main
AFNI controller. At the demand of Ziad Saad.
* Later: and a 'NIML+PO' button below that.
01 Feb 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_purger.c to use a process-specific 3 code suffix after
TIM_ to make it easier to clean up after a crash when multiple
jobs are running.
* Modified mri_genalign.c to patch a memory leak in some floatvec's
not being freed before being reused.
* Modified 3dAllineate.c to use mri_purge() on the output dataset's
sub-bricks as they are being created.
* Modified thd_writedblk.c to deal with datasets that have mri_purge()-ed
sub-bricks. Need to do the same for NIfTI someday, I suppose.
* New function mri_clear() in mri_free.c, to free an MRI_IMAGE's data arra
y
and get rid of it's purged TIM file, if necessary.
26 Jan 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve.c to echo -gltsym files as well as the matrices
they generate.
19 Jan 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve.c and mri_fromstring.c to use '|' as a line
separator in 'SYM:' and '1D:' inputs (as well as '\').
17 Jan 2007, G Chen, 1dSEM, level 4 (SUPER), type 1 (NEW_PROG)
Path analysis (or structural equation modeling) at group level.
See more details on: http://afni.nimh.nih.gov/sscc/gangc/PathAna.html
15 Jan 2007, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Allow replacement of pre-loaded DO and Dsets
When a dataset is reloaded, it replaces the one
already loaded in suma.
15 Jan 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added mri_gamma_rgb_inplace() to mri_to_rgb.c.
* Modified 1dsvd.c to change Left for Right.
10 Jan 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified svd_double() in cs_symeig.c to sort singular values and vectors
.
* Modifed 1dsvd.c to have a '-sort' option.
05 Jan 2007, ZS Saad, imcat, level 2 (MINOR), type 1 (NEW_PROG)
Program to stitch images.
05 Jan 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify mri_read.c to allow 'ragged' input from '1D:' strings
(e.g., for use with 3dDeconvolve).
28 Dec 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify afni_splash.c to save current dataset names and xyz coords in
the startup script.
* Modify afni_driver.c to allow multiple 'keypress=' options to OPEN_WINDO
W.
21 Dec 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Made the change to 'void *' -- no more im.short_data (etc.). Changes
in a bunch more places.
* Modified mri_purger.c to delete extant TIM_* files when exit() happens.
* When AFNI_IMAGE_GLOBALRANGE is yes, don't do redisplay on isqDR_setrange
.
Causes an unpleasant flickering in the image viewer window. Changes
to afni.c (AFNI_range_setter()), imseq.c, etc.
20 Dec 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* mri_purge.c for purging/unpurging MRI_IMAGEs to disk files.
* modify thd_cliplevel.c to do float->int conversion inline, rather
than through a temp image (saves on memory).
* modify mrilib.h to change MRI_BYTE_PTR() (etc.) macro to use
mri_data_pointer() function, which will invoke mri_unpurge()
if necessary. This also entailed changing a lot of functions
to avoid using the im.*_data pointers, which I eventually want
to eliminate entirely.
20 Dec 2006, RC Reynolds, afni_proc.py, level 4 (SUPER), type 1 (NEW_PROG)
program to write complete single subject FMRI processing script
19 Dec 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New constrained optimizer in powell_int.c.
15 Dec 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Made SAVE_FILTERED work with graph windows -- by modifying mri_write_pnm
()
to write through a filter if the output filename starts with '|'.
14 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added SAVE_FILTERED to the roster of AFNI driver commands.
11 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* More changes to 3dBlurToFWHM.c -- de-median and de-MAD before blurring a
nd
before estimating blur, to be somewhat more self-consistent.
* Added SAVE_PNG to the roster of AFNI driver commands.
11 Dec 2006, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 1 (NEW_PROG)
program to convert stim_files to stim_times files
08 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -dem option to 1ddot.c.
07 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added movie saving commands to afni_driver.c.
* Modified 3dFWHMx.c -geom option to add up logs rather than multiply up
results -- for large numbers of sub-bricks, can get overflow the old wa
y.
* Added THD_medmad_bricks() and THD_meansigma_bricks() functions to
thd_median.c -- get location and dispersion statistics at same time,
for speed.
06 Dec 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added ISQ_snap_agif() and ISQ_snap_mpeg().
30 Nov 2006, ZS Saad, suma, level 2 (MINOR), type 0 (GENERAL)
Addition of new Displayable Objects (DO)(ctrl+Alt+s)
Allows display of segments, spheres and other markers
See suma's interactive help 'ctrl+h' for more info.
20 Nov 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Multitudinous changes to 3dBlurToFWHM.c.
15 Nov 2006, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* New program 3dBlurToFWHM.c.
09 Nov 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dFWHM to do what 3dFWHMx does -- not use a voxel in a differen
ce
unless it is in the mask as well.
31 Oct 2006, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* New program 3dFWHMx -- does all sub-bricks.
30 Oct 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified plug_scatplot.c to copy 'Aboot' option from plug_histog.c.
* Modified THD_pearson() stuff in thd_correlate.c to remove mean.
* New program 3dLocalBistat.c -- joint local statistics between 2
datasets.
24 Oct 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dAutomask.c (etc.) to add -peel and -nbhr options, with
also a fix to stupid error made a couple days before.
22 Oct 2006, RC Reynolds, model_demri_3, level 3 (MAJOR), type 1 (NEW_PROG)
NLfim model for Dynamic Enhanced MRI
18 Oct 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Ugh.
* Modified afni_warp.c to only use warp_parent if the dataset being
sliced is an AFNI dataset (not NIfTI, MINC, etc.).
* Modified afni_func.c to print warning when forced view change
when switching datasets or sessions - for Adam Thomas.
12 Oct 2006, RC Reynolds, serial_writer, level 2 (MINOR), type 1 (NEW_PROG)
program to send data from a file, pipe or made up to a given serial port
10 Oct 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dClipLevel.c to allow float input datasets.
* Modified 3drefit.c to make '-TR' option add a timeaxis to a non-3D+time
dataset.
* More changes to 3dAllineate.c.
* Program 3dAcost.c to compute 3dAllineate costs on 2 bricks [now gone].
29 Sep 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* 3dAllineate.c edited to make -linear the default interpolation during
alignment process, and -cubic for the output dataset.
27 Sep 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified correlation ratio in thd_correlate.c to use both Var(y|x) and
Var(x|y) for symmetry between base and target. Seems to make
registration work better.
* Added -check and -master options to 3dAllineate.c.
21 Sep 2006, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* Put 3dAllineate into the distribution. But is not finished.
* Modified plug_nlfit.c to allow AFNI_NLFIM_METHOD to select optimizer.
20 Sep 2006, ZS Saad, DriveSuma, level 3 (MAJOR), type 1 (NEW_PROG)
Program to control SUMA from the command line
08 Sep 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Cosmetic changes to AlphaSim to make '-quiet -quiet' turn off all
stdout printing except numerical table at end.
06 Sep 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to let Ziad/SUMA initialize colors for surfaces.
* Check input datasets for the Mike Beauchamp syndrome.
05 Sep 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Mod mri_read_1D() so that ending filename in ' character causes
transposition. Removed this feature from thd_1Ddset.c to match.
* Changes to AFNI to allow on-the-fly cluster editing.
31 Aug 2006, ZS Saad, AnalyzeTrace, level 1 (MICRO), type 1 (NEW_PROG)
Program to analyze the output of -trace option.
22 Aug 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add WARPDRIVE_ROTMAT_* attribute outputs to 3dWarpDrive.c.
14 Aug 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add pairmax() to parser.f.
08 Aug 2006, RC Reynolds, C++, level 2 (MINOR), type 5 (MODIFY)
afni program compiles in C++ (effort with Rich and Greg Balls)
04 Aug 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add max displacement to 3dvolreg.c.
03 Aug 2006, RC Reynolds, NI_SURF_DSET, level 4 (SUPER), type 0 (GENERAL)
added a new surface dataset format, with read/write ability in AFNI
24 Jul 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* model_linplusort.c (Linear+Ort) for 3dNLfim.c.
21 Jul 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* NEWUOA stuff into 3dNLfim.c and simplex.c.
18 Jul 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Fixed -xyzsave option in 3drefit.c to make multiple datasets match.
17 Jul 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added options -keepcen and -xyzscale to 3drefit.c.
05 Jul 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_dicom.c to deal with big-endian file transfer syntax.
* Also check for overflow in 16-bit unsigned integer DICOM images.
02 Jul 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Inserted Powell's NEWUOA code into AFNI libmri.a.
19 Jun 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed flip_memplot() error in coxplot/plot_cox.c, where non-line element
s
were being flipped when they shouldn't be.
01 Jun 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New AFNI splash photograph!
* imseq.c now doesn't append '.jpg' if Save filename already ends in it.
24 Apr 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -sum option to 3dTstat.c.
13 Apr 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* mri_matrix_evalrpn() ==> 1dmatcalc.c and 3dmatcalc.c.
* Modify mri_fromstring.c to allow 1D:... generation of multiple columns.
10 Apr 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -polort option to 3dDetrend.c.
05 Apr 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -frugal option to 3dZcat.c.
04 Apr 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to 3dInvFMRI.c: -mapwt, better help, God knows what else.
31 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* to3d.c: if first filename is 'something.img', check if 'something.hdr'
exists, and if so, suggest that the .hdr file is more likely to be
what they want to input.
* Added '-method' and smoothing options to 3dInvFMRI.c.
29 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* First version of 3dInvFMRI.c.
28 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dDeconvolve.c to set ival=-1 on various inputs, before
sscanf()-ing it, so that bad values give error messages.
* Also add -x1D option to 3dDeconvolve.c, to save X matrix to a .1D file.
25 Mar 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify matrix.c and matrix_f.c to unroll matrix-vector multiply by
four rather than two, after profiling with Shark on the MacIntel
(which showed that loop overhead was a significant factor).
24 Mar 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify thd_niftiread.c to prioritize sform over qform (to match
other packages), but to allow user to set environment variable
NIFTI_FORM_PRIORITY to 'Q' or 'S' to signify the priority.
* Also, if both qform and sform are present, check to see if they
have the same handedness -- if not, print a warning message.
20 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dAutomask.c and thd_automask.c to add new -clfrac option.
* Modify matrix_f.c to use Solaris BLAS in single precision.
13 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Checks in afni_func.c, adwarp.c, and thd_writedblk.c for free disk
space, just before actual writing of .BRIK file.
* 3dTwotoComplex.c from 3dThreetoRGB.c
10 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Mods to 3dcalc.c to allow use of complex-valued dataset on input.
09 Mar 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* A little more dynamical action when a few environment variables are
changed via external scripts.
* WAV_duration in waver.c was an int, not a double (thanks, Rasmus!).
08 Mar 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Bug fix in afni_version.c for MOTD failure when network down.
* Modify PERROR() macro in thd_iochan.c to NOT print so many duplicate
messages.
* Modified afni_environ.c so that setting AFNI_ALWAYS_LOCK immediately
changes the lock situation.
25 Jan 2006, RC Reynolds, model_michaelis_menton, level 3 (MAJOR), type 1 (NEW_PROG)
NLfim model function for ethanol studies
09 Jan 2006, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* mri_warp3D_align.c now will revert to 'best' fit if final fit is
much worse in RMS terms.
30 Dec 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Web browser stuff in afni.h, afni_func.c, afni_widg.c.
28 Dec 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* fixes to mri_warp3D_align.c and thd_automask.c to deal with problems
with -parfix, and with doing mask stuff on 2D images.
21 Dec 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* afni_broutext.h
06 Dec 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* -coarserot in 3dWarpDrive.c, too.
02 Dec 2005, RC Reynolds, ANOVA, level 5 (SUPERDUPER), type 5 (MODIFY)
changed variance computations in 3dANOVA programs to not assume sphericity
For details, see http://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html .
01 Dec 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* -coarserot in 3dvolreg.c
01 Dec 2005, G Chen, 3dANOVA3, level 3 (MAJOR), type 2 (NEW_OPT)
New options to run 2nd-order general linear contrasts in 3dANOVA3.
See more details on: http://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html
30 Nov 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Change sub-bricks stuff in afni_driver.c.
29 Nov 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Message of the Day (motd) stuff.
22 Nov 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* [l] in imseq.c.
18 Nov 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* AUTHOR AUTHOR.
14 Nov 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to afni_splash.c to try to avoid the 'Mr Freeze' bug (e.g.,
unrealize image viewer rather than destroy it).
08 Nov 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* rint(x) -> rint(x+.00001) in edt_coerce.c, to avoid an artifact in
3dMean.c when the number of averages is a small even integer.
02 Nov 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Another small change to imseq.[ch] to the winfo label.
31 Oct 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Small changes to imseq.c, to display 'Min2Max' and 's=%d' modes, and
to update winfo label when Keypress 'l' is used.
26 Oct 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Mod to symeig_3 (in cs_symeig.c) to avoid problems that are invisible.
* Mod to plot_x11.c (in coxplot/) and 1dgrayplot.c, to plot correctly.
25 Oct 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Makefiles for macosx_10.4_G5 and solaris29_suncc_64.
24 Oct 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve.c to use mmap() with MAP_ANON instead of shmem
for inter-process storage. Can go beyond 2 GB barrier this way,
on 64-bit compiles.
21 Oct 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dToutcount.c to check for float_scan type errors.
18 Oct 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -usetemp option to 3dcalc.c.
* Added some timing delays to popup/popdowns.
11 Oct 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_niftiwrite.c and 3dAFNItoNIFTI.c so that specifying a .hdr
output filename means you get a .hdr/.img NIfTI-1.1 file pair. Note
that thd_analyzeread.c and thd_niftiread.c already allow for .hdr/.img
NIfTI-1.1 file pair inputs.
11 Oct 2005, RC Reynolds, 3dmaxima, level 3 (MAJOR), type 1 (NEW_PROG)
command-line version of maxima plugin
06 Oct 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified edt_blur.c to skip min/max clip calculations when all direction
s
are done with FIR.
* Modified thd_dsetatr.c to write BRICK_STATSYM attribute not just for
func bucket datasets but for fitt, fift (etc.) legacy types.
* Fixed bug in 3dbucfim.c where the stat_aux array was possibly loaded
with illegal array access values.
04 Oct 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified edt_blur.c to do small Gaussian blurs in real-space, with the
fir_blur?() functions. Also added FIR_blur_volume() function to allow
user to invoke FIR explicitly, rather than implicitly.
* Add 'TRACE' command to afni_driver.c.
30 Sep 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* 2x2 and 3x3 special cases for cs_symeig.c.
28 Sep 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to 3dWarpDrive.c to summarize results (-summ) and to prevent ste
ps
that make the RMS error much worse.
23 Sep 2005, G Chen, 3dANOVA2 and 3dANOVA3, level 4 (SUPER), type 4 (BUG_FIX)
Significant modifications in 3dANOVA2 and 3dANOVA3
The changes were made to avoid statistics inflation for general linear
contrasts when coefficients don't add up to 0. See more details at
http://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html
21 Sep 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified thd_writedset.c and 3dAFNItoNIFTI.c so that if AFNI_AUTOGZIP is
YES, then .nii.gz files will be written instead of .nii files.
01 Sep 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Fixed 3drotate.c so that '-rotate 0 0 0' doesn't fail.
26 Aug 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* THD_check_AFNI_version() function in thd_vcheck.c. Use this in a few
popular '3d' programs.
24 Aug 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Ugghh. More SVD trouble.
23 Aug 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* -FILE option for waver.c.
* In imseq.c: 's' (sharpen), 'D', 'M', 'S' (Disp, Mont, Save).
22 Aug 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New program 3dLocalstat.
* In imseq.c: 'm' (toggle Min-to-Max), 'a' (fix aspect), 'l' (LR mirror).
* '%s' in thd_compress.h means that you can now read .gz files with spaces
in their names.
15 Aug 2005, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* From now on, unless AFNI_ALLOW_MILLISECONDS is set to YES, AFNI programs
will
convert MSEC time unit datasets to SEC on input and output.
12 Aug 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Start editing 3dDeconvolve.c to have -slice_base option, for slice-depen
dent
baseline regressors. [never finished]
10 Aug 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified cat_matvec.c to allow ::WARP_DATA input, and MATRIX() output.
08 Aug 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'AFNI Version Check!' logo to afni.c & afni_widg.c in case user is
out of date.
03 Aug 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dWarp.c to save WARPDRIVE_MATVEC_ attributes into the header
of the output, assuming that they were used (with '-matparent') on inpu
t.
* Modified 3drefit.c to add '-atrcopy' and '-atrstring' options to copy an
d
set attributes.
29 Jul 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added '-com' option to afni.c.
* Added grapher windows to SAVE_JPEG in afni_driver.c.
28 Jul 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added stuff to afni_driver.c (SAVE_JPEG, SET_DICOM_XYZ, SET_SPM_XYZ,
SET_IJK, SET_XHAIRS), and imseq.[ch].
27 Jul 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Removed -ffast-math from Makefile.linux_gcc32, since it seems to cause
problems in eis_svd.c (at the least).
25 Jul 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program im2niml.c, and '-p' option to aiv.c.
19 Jul 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* 3dWarpdrive '-bilinear_general' now works. Usefulness is another questi
on.
* Fixed 'EMPTY IMAGE' display problem in afni_warp.c -- DSET_INMEMORY()
macro in 3ddata.h needed to check for STORAGE_UNDEFINED.
13 Jul 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify afni_widg.c and afni.c so that a Button-3 click on an Image or
Graph button will recall the open window from offscreen purgatory.
12 Jul 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify thd_1Ddset.c so that a 1D filename ending in a ' character will b
e
transposed on input (as a dataset), so that columnar datasets can be
treated as time, without using 1dtranspose and a temporary file. Also,
if prefix starts with '-' character, will write .1D datasets to stdout.
08 Jul 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed Makefile.macosx_10.? to suppress multiply-defined symbol errors.
* Modified 3drefit.c and 3dcopy.c to add '-denote' option, to remove notes
and other potentially identifying attributes.
07 Jul 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dWarpDrive.c to save affine matrix to output file header attri
butes
(named WARPDRIVE_MATVEC_*), and also to base the coordinates on the act
ual
dataset rather than the center of the volume.
* Modified 3dWarp.c to read matrix from header attribute WARPDRIVE_MATVEC_
*.
05 Jul 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dAFNItoANALYZE.c to scale TR by 0.001 if units are msec.
* Modified thd_writeatr.c and thd_writedset.c to correctly write NIML-styl
e
.HEAD file from to3d.c (the blk->parent pointer wasn't set correctly).
05 Jul 2005, RC Reynolds, Dimon, level 4 (SUPER), type 1 (NEW_PROG)
program to monitor real-time acquisition of DICOM images
17 Jun 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add overlay labels (accum_lab stuff) to plug_crender.c. Added by the
right-click popup on the 'Accumulate' label.
10 Jun 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to niml/niml_stream.c to make atexit() stuff work properly
when NI_stream_reopen() is used (this is Ziad's fault, of course).
09 Jun 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Warnings when adwarp.c or afni_func.c is about to write a .BRIK file
over 500 MB in size.
08 Jun 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* A number of small changes to get AFNI to compile on Tiger.
06 Jun 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'Brodmann Areas' image popup to the 'Hidden' popup menu.
03 Jun 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in 3dAFNIto3D; if input is a .1D file and no -prefix was given
,
the output file would overwrite the input!
* Modified the .3D I/O functions to
(a) allow binary format for the data;
(b) allow a time step to indicate 3D+time status;
(c) if the output prefix ends in '.3D', automatically write this format
.
Binary vs text format is setup by environment variable AFNI_3D_BINARY.
prefix
* Moved AFNI_setenv() function to afni_environ.c for librariness.
02 Jun 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify thd_nimlatr.c to split large String attributes into multiple
substrings when using NIML, so as to avoid buffer size problems.
* Fixed bug in niml/niml_stat.c decoding of strings such as 'Ftest(3,7)'
(forgot to skip the comma!).
* Remove AFNI_niml_atexit() from afni_niml.c since it is now redundant
with the atexit stuff in niml/niml_stream.c (oopsie).
01 Jun 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifications to thd_atr.c, etc., to allow .HEAD files to be stored
using XML.
* Warn user when ~/.afni.log file goes over 100 MB (the Kevin Murphy bug).
31 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified various things (like thd_nimlatr.c) to change names of some
NIML attributes, in concordance with the treaty reached today with
Ziad Saad.
24 May 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add 'i' and 'I' keystrokes to afni_graph.c, to move init_ignore down/up.
23 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add checks for data axes mismatch when inputting multiple datasets to
3dcalc.c, 3dTcat.c, 3dbucket.c, and thd_opentcat.c. Because of
stoopid lusers.
* Add 'Ignore xxx' label to bottom of afni_graph.c window, for stupid
users like me.
18 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add '-dicom' and '-spm' options to 3dcalc.c.
* Add a couple of warnings for stupid new users.
* Fix parser.f so that acos(1) and asin(1) work (tested .LT., not .LE.).
17 May 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'Draw ROI plugin' menu item to image viewer popup, in afni.[ch].
16 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Some minor changes to help AFNI compile on Tiger, as reported by Frank
Haist of UCSD.
13 May 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'xamplitude' option to waver -tstim option.
* Oops. Fixed bug in 3dDeconvolve for -iresp/-sresp options: malloc-ed
the 'hout' float** array with sizeof(float) not sizeof(float*), which
doesn't work too good on 64 bit systems.
* Modified 1dplot.c to
(a) allow reading up to 10000 numbers on a line from stdin, and
(b) transpose input file if it has only 1 line, so that a long
single line of numbers becomes a decent plot.
12 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'NIfTI_num' signature to thd_niftiwrite.c and thd_niftiread.c.
11 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify the NIfTI-1.1 extension stuff to be more robust. Also add
environment variable AFNI_NIFTI_NOEXT to turn extensions off, and
use this to provide a '-pure' option to 3dAFNItoNIFTI.c.
10 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify thd_initdblk.c, thd_niftiread.c, thd_niftiwrite.c to store AFNI
header data in a NIfTI-1.1 extension, making it more feasible to use
.nii datasets in AFNI as a primary storage mechanism.
09 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify plug_nudge.c to deal with RGB-valued datasets.
06 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* non-AFNI datasets (e.g., .nii files) now have ID code set via hashing
their realpath, rather than a random ID code.
* Modify EDIT_dset_items() to change the brick_name correctly when the
new prefix ends in '.nii' or '.nii.gz'.
* Modify a bunch of programs that print 'Writing dataset' messages to
always use the DSET_BRIKNAME() macro, for consistency.
04 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Oops. Fix atexit() bug in niml/niml_stream.c -- had logic inverted on
when to remove a stream from the 'open list'.
03 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* More changes to 3drotate.c along the same line.
* Edit afni.c to set width of bucket label AVs (in Define Overlay) based o
n
max width of input sub-brick labels, for each dataset separately.
02 May 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added plot of least squares overlay line to the Scatterplot plugin.
* 3drotate.c now records the applied matvec into the AFNI header attribute
s.
29 Apr 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Moved extras printout in 3dDeconvolve -nodata to be optional with
an environment variable.
* Fixed bug in range locking in afni_lock.c -- if range is locked but
only one controller open, couldn't turn autoRange on.
28 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve to add -basis_normall option, and a couple of
other minor tweaks.
27 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve.c to allow -stim_times to be used with -nodata.
To do this, you use '-nodata NT TR' to specify the number of time
points and their TR.
* Modified imseq.c to make up/down movement of stroking affect RGB,
additively, much as left/right does multiplicatively.
26 Apr 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to apply 0D and 2D transforms to RGB images (that is,
in the intensity channel). And afni_func.c to apply to RGB overlays.
25 Apr 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Minor changes to NIML.
* Gamma variation allowed for RGB display in imseq.c.
25 Apr 2005, RC Reynolds, NIFTI, level 4 (SUPER), type 0 (GENERAL)
AFNI can read and write NIFTI datasets (effort with Bob and Rich)
21 Apr 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Where AFNI_COLORSCALE_0x is allowed in pbar.c, also check for
AFNI_COLORSCALE_x and AFNI_COLORSCALE_Ox, to allow for stupid users.
Similar changes in a few other places, as well.
* Modified niml/niml_rowtype.c and niml_stream.c to re-enable input
of Base64-encoded data elements (capability had been lost with
the advent of rowtypes and var-dim arrays).
20 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to let 0 values in the overlay image get color
if environment variable AFNI_OVERLAY_ZERO is set to YES.
19 Apr 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified niml/niml_element.c to add NI_alter_veclen() function, and
NI_insert_string() function.
* Modified plug_tag.c and a couple others to allow func datasets as
inputs, as well as anats.
18 Apr 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_write.c functions to write to stdout if the output
filename is the string '-'. This mod affects mri_write_pnm(),
mri_write(), and mri_write_ascii(). Indirectly affects program
imupsam.c.
15 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -automask option in 3dDeconvolve.c.
* Add mri_write_jpg() to mri_write.c. Now mri_write() automatically
writes a .jpg file for RGB and BYTE images if the filename ends
in '.jpg'.
13 Apr 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added one to the count of the basis function -iresp and -sresp
counts, to ensure getting the last point!
07 Apr 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_niftiread.c to use the NBL functions in rickr's
nifti1_io.c to read the data from a .nii file -- this makes
.nii.gz files work as well, automagically.
* Fixed bug in imseq.c -- logic for taking the button box value
for animations to/from the integer flags was bad in the case
where an aGif filter doesn't exist.
* Fixed bug in thd_niftiwrite.c -- 'if( nparam = 3)' was amended
to '=='.
* Modified thd_niftiwrite.c to allow output of func bucket as
the 'u' dimension.
06 Apr 2005, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* Added '.nii' output feature to THD_writedset() function, and did
a few other similar things hither and yon.
04 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'Pleg' function to parser and thence to 3dcalc, etc.
31 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Oops. Fixed bug in afni_niml.c wrt processing
instruction: needed to put the command into an attribute.
* Added a 1 ms wait to niml/niml_stream.c when a tcp: or shm: stream
is closed. This is to let the application on the other end have
a decent interval to fetch any just-transmitted data.
* Modified thd_opendset.c to NOT print an error message when trying to
open a non-existent file -- now just prints a message if the file
exists but has no data.
30 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in AFNI_range_label() in afni_func.c about brick range
setup change of yesterday (forgot to initialize stats_*_ok).
29 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to call AFNI_reset_func_range() at start of
AFNI_func_overlay() to make sure brick ranges are set properly
for display.
* Modified fim+.c and 3dfim+.c to allow polort > 2, by using Legendre
polynomials for the baseline model.
* Fixed bug in NIML, where the new 'outmode' field in elements wasn't
being initialized to -1 like it should have been.
28 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to the AFNI update script written out in afni_version.c.
* Modified total_bytes field in datablock structure to be int64_t rather
than int, to better deal with huge datasets. Modified a lot of places
that refer to this field, especially places dealing with reading and
writing datasets.
* Modified thd_loaddblk.c to auto-update brick statistics for non-AFNI
datasets.
22 Mar 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* mean(), stdev(), and sem() for parser and 3dcalc.
* Modify Ziad's plugout_drive.c '-com' option to execute commands in
order given, rather than the reverse order.
* Fix REDISPLAY in afni_driver.c (oopsie).
* Added '' input to afni_niml.c, to store as .1D files.
* Added '-Dname=val' option to afni.c (set environment variables).
21 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Edgize the overlay.
18 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Finished up NIML bulk transfer of datasets to AFNI, etc.
11 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed up the NIML-ization of datasets, and their transmission into
AFNI.
09 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New functions to (a) write dataset struct stuff into attributes (moved
out of THD_write_dataset and THD_write_datablock); to (b) convert
dataset attributes to/from a NIML group; to (c) populate datablock
from attributes, rather than do so on-the-fly as they are read in.
08 Mar 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Including retroicor stuff from Fred Tam.
07 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Ooops. Have to '#include ' into matrix_f.h to make sure
DONT_USE_MATRIX_MAT is defined.
04 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Further matrix.c changes: store as one array, not an array-of-arrays,
except on Solaris, where the array-of-array approach is faster(!?).
02 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Further matrix.c changes for BLAS-1 on Solaris.
01 Mar 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified matrix.c and matrix_f.c to use BLAS-1 on the SGI Altix.
28 Feb 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Oops -- used '&&' instead of '||' in byte swap test in new thd_ctfread.c
.
* More surgery on NIML registry and Htables.
26 Feb 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_ctfread.c to seek backwards from end rather than forwards;
this
makes it work with the new CTF svl format.
25 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -min option to 3dmaskave.c.
* Fixed memory leak in niml_dtable.c (forgot to free second copies of stri
ngs).
* New niml_registry.c stuff, for allocating 'registered' structs.
24 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dmaskave.c to have -max option.
* Modified niml/ functions to generalize NI_group elements so that any
element name is OK, provided attribute ni_form='group' is present.
23 Feb 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified to3d.c to accept -Torg option. Also to thd_info.c to print
out the ttorg field.
22 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dTshift.c and to3d.c to have new 'alt+z2' option.
* New program 3dMedianFilter.
* Added I:*.1D stuff to 3dcalc.c.
18 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified afni_driver.c, imseq.c, and afni_graph.c to add 'keypress='
modifiers to the OPEN_WINDOW commands for driving AFNI.
16 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dhistog.c to remove -thr stuff and add -doall stuff.
07 Feb 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in Deconvolve.c with removing mean of -stim_base columns.
01 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -redo_bstat option to 3drefit.c.
24 Jan 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added environment variable AFNI_SLAVE_THRTIME to afni.c.
14 Jan 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added program whereami, from Mike Angstadt of U Chicago.
07 Jan 2005, RC Reynolds, nifti_tool, level 4 (SUPER), type 1 (NEW_PROG)
program to directly manipulate or compare NIFTI dataset headers
07 Jan 2005, RC Reynolds, NIFTI, level 4 (SUPER), type 0 (GENERAL)
initial release of NIFTI library
06 Jan 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to free the pen_bbox and labsz_av when destroying an im
age
viewer -- somehow these got overlooked in ISQ_free_alldata().
05 Jan 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 1dsvd.c to add -1Dright option.
* Fixed bug in 1dplot.c -stdin option: failed to skip leading blanks prope
rly
when scanning input lines for '#' comment characters! (Stupid)
* Modified imseq.[ch] to add saving of overlay MEM_plotdata stuff with the
recorder, as well as the images.
04 Jan 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_warp3D_align.c and 3dWarpDrive.c to fix up some issues with
-twopass on small (EPI-sized) bricks and to add -1Dfile option.
03 Jan 2005, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_imcount() in mri_read.c to not do '3D:' counting on a file
unless there is actually a colon in the filename! D'oh.
22 Dec 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Incorporated 3dMean.c changes from Mike Beauchamp to add standard deviat
ion
option.
* Fixed stupid scale_thr bug in afni_func.c.
21 Dec 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to allow dataset 'label2' field to be displayed in
window titlebars, instead of filenames. Also affected: afni_pplug_env.c
and 3drefit.c (to let user change label2 field).
* Replaced VERSION with AFNI_label.h header, generated by script Ctag.
20 Dec 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to allow user to threshold RGB-valued overlays.
17 Dec 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* AFNI_faceup() in afni_splash.c and on the hidden popup menu.
09 Dec 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* PURGE_MEMORY addition to afni_driver.c.
06 Dec 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed '' dataset input without '[...]' input to not print a warnin
g
message about the lack of sub-brick subscripts.
* Modified 3dmaskave.c to add '-mask SELF' option.
01 Dec 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -twopass option to 3dWarpDrive, etc.
30 Nov 2004, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* First version of 3dWarpDrive released.
* 3dcalc now prints a warning if outputing a byte-valued dataset when the
calculated results had some negative values.
16 Nov 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to print warnings when it can't find Save filter progra
ms.
03 Nov 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Some changes to 3dAnhist.c for Lukas and Katie.
29 Oct 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dfim+.c to make Spearman and Quadrant CC bricks fico.
* Modified niml/niml_rowtype.c to auto-define VEC_basictype_len types
when first referenced.
22 Oct 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifed thd_shear3d.c to use true SVD in computing the rotation for
3dTagalign, rather than the symmetric eigensolution method.
21 Oct 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Also added ISPOSITIVE and ISNEGATIVE functions to parser.f
20 Oct 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified parser.f to add NOTZERO, ISZERO, and EQUALS functions.
06 Oct 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.[ch] to add a chooser to set the thickness of
'Thick' lines in the graph viewers (on the 'Opt->Colors, Etc.' menu).
Also, afni.c to add AFNI_graph_gthick to initialize this value.
05 Oct 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to write animated GIF files with a fixed colormap,
to avoid color flashing when (e.g.) rotating a volume rendering.
04 Oct 2004, RC Reynolds, vol2surf, level 4 (SUPER), type 0 (GENERAL)
added vol2surf interface for real-time mapping from afni to suma
15 Sep 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New function THD_get_voxel() in thd_loaddblk.c, returns a float for a
single voxel (not very efficient to use this in mass).
* Used the above in thd_fdto1D.c to deal with returning time series from
datasets with mismatched sub-brick types.
* Also, print a warning for such datasets in thd_initdblk.c.
09 Sep 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_version.c to use TCP/IP to communicate with version
sub-process rather than shared memory.
07 Sep 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed some stuff in the -help output of afni.c.
02 Sep 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_symbolize.c to correctly use the intlist() function.
* Patched thd_auxdata.c and thd_initdblk.c not to create brick labels
over 32 characters in length. (Someone who shall remain nameless
created one several thousand characters long, and thd_info.c didn't
like that much.)
30 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve.c basis_write_response() to be more efficient (don
't
evaluate basis expressions so often).
* Added basis_write_sresp() to 3dDeconvolve.c to write standard deviation
of the IRFs.
29 Aug 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added EXPR(bot,top) basis function to 3dDeconvolve.c.
23 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug with polort=-1; program creates a baseline model matrix with
0 columns, and matrix_psinv() didn't like that.
* Add basis_write_response() to 3dDeconvolve.c to actually write out the
computed IRF for symbolic models.
19 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* eis_svd.c sometimes works wrong with 'gcc -O', so modified Makefile.INCL
UDE
and eispack/Makefile to turn optimization off for this file.
12 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified Deconvolve.c and 3dDeconvolve.c to remove mean from baseline
timeseries if polort>0, and -nodmbase option is not given.
* 3dDeconvolve saga: Generate response vectors from stimulus timing and
user-specified model.
11 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added environment variable AFNI_3dDeconvolve_nodup to 3dDeconvolve.c,
to stop processing if duplicate columns are discovered.
10 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Started work on 3dDeconvolve.c to add -stim_times option for direct
input of models to fit.
* Modified mri_read_ascii_ragged() to read a '*' character as a fill,
thus allowing lines with no entries or intermediate missing entries.
06 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in 3dDeconvolve.c where -cbucket bricks were colliding with
-bucket bricks, vi bar[] and attach_sub_brick().
05 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Polished up the 3dDeconvolve.c changes.
* Added 'README.environment' text to Datamode->Misc menu in AFNI.
04 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* At long last, removed the ill-fated 'merger' stuff from 3ddata.h and
all AFNI functions.
* Added THD_open_tcat() in thd_opentcat.c, to open a list of datasets as
on long 3D+time dataset. Also modified 3ddata.h, THD_open_dataset(),
and so forth.
* Modified 3dDeconvolve.c to use this feature to allow input catenation
(if the input_filename field has blanks in it).
03 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified matrix_print() in matrix.c and matrix_f.c to print shorter stri
ngs
when the matrix comprises all 1 digit integers.
* Modified 3dDeconvolve.c to print -gltsym matrices when AFNI_GLTSYM_PRINT
environment variable is YES.
* Modified matrix_f.c to use Altivec on Mac for matrix-vector multiplies.
Adds about 10% to speed on G5, over the loop unrolling from yesterday.
02 Aug 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified matrix_f.c to include loop unrolling found in matrix.c.
* Modified mri_symbolize.c and 3dDeconvolve.c to use '[[...]]' subscriptin
g
for -gltsym multi-row expansion.
29 Jul 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added mri_symbolize.c, and -gltsym option to 3dDeconvolve.
28 Jul 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Finished (I hope) addition of -xsave and -xrestore options to 3dDeconvol
ve.
* Fixed (I hope) bug in AFNI_setup_viewing() in afni.c, where the ULay
sub-brick chooser optmenu wouldn't be configured correctly in controlle
r
[B] (etc.) due to anat_old check not also checking im3d_old.
* Modified mri_read_ascii() and my_fgets() in mri_read.c to not malloc/fre
e
line buffer for each line read. Also, removed the '' feature.
* Added mri_read_ascii_ragged() to mri_read.c.
27 Jul 2004, G Chen, PathAna, level 4 (SUPER), type 1 (NEW_PROG)
A Matlab package that runs group analysis of up to 5-way ANOVA
This package adopts the conventional ANOVA approach to handling gorup
analysis. And it requires Statistics Toolbox other than the basic Matlab.
See more details on: http://afni.nimh.nih.gov/sscc/gangc
27 Jul 2004, G Chen, IndiAna, level 4 (SUPER), type 1 (NEW_PROG)
A Matlab package for individual subject analysis
See more details at http://afni.nimh.nih.gov/sscc/gangc
22 Jul 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_drawing.c and coxplot/plot_cox.c to allow for opacity.
Used this in -xjpeg option in 3dDeconvolve.c.
21 Jul 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modifed MCM_get_intlist() to print error messages when the user inputs
values off the top end of the range, instead of silently turning them
into the top (stupid users).
* Modified afni_fimmer.c to correctly use scaling factors if present in
the time series data (oops, for about 8 years).
* Added printout of pseudo-inverse to 1dsvd.c.
* Added -svd option to 3dDeconvolve. Also, if SVD is on, then DON'T
remove all zero stimuli from the list.
* Added -xjpeg option to 3dDeconvolve: grayplot of X matrix.
20 Jul 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_get1D.c to limit loading of 1D files in AFNI to a max size
set by environment variable AFNI_MAX_1DSIZE (default 123K).
* Modified mri_read_ascii() in mri_read.c to use the 'n@val' method for
value duplication. Also modified my_fgets() to return a duplicate
of the previous line if the first two nonblank characters on the line
are ''.
19 Jul 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified matrix.c and RegAna.c to do matrix solutions with pseudo-invers
e
from SVD, rather than normal equations.
* Adapted svd.f into eis_svd.c a little more, and also wrote a wrapper
function into cs_symeig.c, and a test program 1dsvd.
16 Jul 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified Deconvolve.c to use correctly normalized Legendre polynomials,
for potential ease-of-use for people who want to know what the
baseline functions are.
15 Jul 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve.c and Deconvolve.c to have -legendre option, for
use of better polynomials for the baseline estimation.
* Modified matrix.c and matrix_f.c to have matrix_inverse_dsc() function,
to use diagonal scaling before/after the matrix inversion. Modified
RegAna.c to use this function, to avoid stupid scaling issues.
Also modified condition number calculation to take this into account.
14 Jul 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve.c to make some basic checks
- equal filenames for -stim_file options
- zero columns in X matrix
- collinear column pairs in X matrix
- compute matrix condition number
* Modified matrix.[ch] and matrix_f.[ch] to support this stuff.
* Disabled 3dDeconvolve_f binary, sort of.
08 Jul 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read.c to allow line lengths of up to 512K in *.1D files.
* Modified coxplot/plot_ts.c to correctly remove labels from separate plot
boxes if input nnayy==0.
* Modified 1dgrayplot.c to have new '-sep' option.
23 Jun 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified AFNI_leave_EV in bbox.c to avoid memory leak (must free up the
retrieved textfield string if an early exit is taken).
22 Jun 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to set various environment variables to new defaults
- crosshair lines are on instead of off
- controllers are locked instead of unlocked
- save square is on instead of off
21 Jun 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dclust -help to print out info about coordinate systems.
* Modified afni_func.c to add environment variable AFNI_BUCKET_LABELSIZE
to modify bucket label sizes.
08 Jun 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added call to THD_copy_auxdata() to mri_warp3D.c, and -copyaux option to
3drefit.c
* Added AFNI_IMAGE_SAVESQUARE environment variable to imseq.c; added
functions to mri_warp.c to implement re-aspectizationing.
12 May 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dvolreg.c to make -sinit turn scale init off for -twopass.
11 May 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to apply Zero Color to RGB images.
09 Apr 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed lack of fclose() in ts.c (a 10 year old bug!).
08 Apr 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* AFNI_X11_REDECORATE in xutil.h and afni_pplug_env.c, to replace MCW_isit
mwm().
05 Apr 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixes to afni_graph.c to spackle over unexplainable crashes on Mac when
a timeseries chooser is opened and later the graph window is closed.
02 Apr 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Mods to fix auto_grid()-ing in afni_graph.[ch].
31 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Weird Mac problem: afni_graph.c crashes when destroying graph viewer
Widgets, but only after the timeseries chooser is popped up. Stupid
solution is to only unrealize widgets if this chooser was opened by
the user. WTF?
31 Mar 2004, RC Reynolds, serial_helper, level 3 (MAJOR), type 1 (NEW_PROG)
program to pass realtime registration params from TCP to serial port
24 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify Intracranial.c to deal with an optimizing bug on Mac OS X
-- doesn't work well with large auto arrays.
23 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* 3dZeropad.c gets new -RL, -AP, -SI options.
22 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* AFNI_SLAVE_FUNCTIME in afni.c.
* Modified 3dvolreg.c to make -wtrim always be on, and to scale init
for the twopass iteration.
21 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* AFNI_DISABLE_CURSORS in xutil.c.
19 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added vector chooser to bbox.[ch] and used in afni_graph.[ch] for choosi
ng
graph pin top and bottom together.
18 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed plug_nth_dataset.c to right fill short time series with WAY_BIG,
and then afni_graph.c to not plot these tails in the dplot overlay.
* Modified afni_graph.[ch] to allow pin_bot as well as pin_top (ugh).
17 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* AFNI_GRAPH_AUTOGRID variable in afni_graph.c.
* Fixed memory estimate in 3dAutoTcorrelate.c.
15 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* More 'Anatomy' -> 'Underlay' and 'Function' -> 'Overlay' stuff.
* Added optmenu_EV_fixup() to bbox.c - change cursor arrow on optmenu popu
ps.
12 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.[ch], afni_widg.c, to put popup DICOM/SPM coordinate menu
on crosshair coordinate label.
* 'Anatomy' -> 'Underlay' and 'Function' -> 'Overlay' in several places.
11 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified use of SPM originator field in thd_analyzeread.c to subtract
1 from indexes.
* Modified mri_warp3D.c and 3dWarp.c to do MNI<->TTA transforms.
* Don't need '-eval' option on ccalc command line anymore.
09 Mar 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'ms' time unit selection to 3dcalc.c -dt/-taxis options.
29 Feb 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Re-fixed the thd_shear3d.c bug of 24,FEB,2004, since it was wrong.
24 Feb 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in thd_sheard3d.c, when input matrix to rot_to_shear_matvec()
is identity, could get a bad shear. In this case, just manually put
the correct shear into place.
23 Feb 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added range locking to afni_lock.c and afni_func.c.
* Added tick marks to imseq.c.
* Rick Reynolds added NN interpolation option for zooming to mri_dup.c.
19 Feb 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -mask and -srad and 5th-value=radius features to 3dUndump.c.
12 Feb 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Oooops. '\noesc' should be '\\noesc' in several places. My bad.
* Modified mri_read.c to allow GE 'IMGF' flag to be anywhere in 1st 4K
of file, if file starts with 'GEMS' instead of 'IMGF'.
11 Feb 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in afni_graph.c about average time series, when graph is
too short. I think. [cf. 27,JAN,2004]
10 Feb 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Made threshold locking move sliders during drag, not just end of drag.
Also change pval at bottom of locked sliders during drag. Also put
Edit Environment button on top-of-pbar popup menu.
07 Feb 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added pbar locking (via environment variable AFNI_PBAR_LOCK), and
threshold p-value locking.
* Added AFNI_DISP_SCROLLBARS to afni_pplug_env.c, to control if Disp
menu in image viewer gets scrollbars.
06 Feb 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added threshold locking (via environment variable AFNI_THRESH_LOCK).
Also, moved lock code from afni.c to new file afni_lock.c.
29 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added the cute little diagonal 'AFNI' to various windows.
* Modified rtfeedme.c to add the '-gyr' option to test GRAPH_[XY]RANGE.
28 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added hints to various menu items that were lacking them in afni_graph.c
.
27 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'WinAver' feature to afni_graph.[ch] and afni.c. This shows the
'ideal' waveform as the average of all the timeseries in a graphing
window.
* Modified afni.[ch] and afni_widg.c to set a flag in each im3d, so that
if it is created when the dummy dataset is present, then when a real
dataset becomes available, the controller will get set to the middle
of THAT dataset's coordinates, rather than the dummy's middle. This
is useful for realtime imaging (which is why the dummy is there).
23 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifications to put surfaces into sessions rather than directories.
* Modified ISQ_show_zoom() in imseq.c to avoid infinite recursion that
seems to happen when user zooms, crops, then changes image fraction
(with the 'i' arrows). WTF?
* Modified imseq.[ch] to NOT place dialog near changed window when closing
the Montage control dialog, since that hangs up for a while on the Mac.
* Modified afni.c to make sure surface boxes are plotted with line
thickness zero.
16 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dFDR.c to produce some output when -input1D option is used!
15 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c so that -skip_afnirc option works again (was being screw
ed
up in machdep() function). Also added a couple friends.
* When re-f2c-ing a .f file, must remove declarations of built-in function
s
from the C code, since they cause the g++ compilation to fail to link.
Also, in coxplot/*.c functions, must manually change the COMMON struct
definitions to extern.
* Added SHORTIZE() and BYTEIZE() to mri_to_short.c and mri_to_byte.c to
avoid integer overflow problems when scaling and/or changing data types
.
14 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot/pwritf.f to allow color changes in the text, and to
allow disabling of the escape mechanism (so filenames with '_' are OK).
* Modified 3drotate.c, 3AnatNudge.c, 3dLRflip.c, 3dTagalign.c, 3copy.c to
allow processing of non-AFNI (e.g., MINC) datasets. The problem was
that these program open/load a dataset, modify it in-place, rename it,
then write it out. That won't quite work for non-AFNI datasets, since
the dataset is still marked as being MINC (say), and we can't write
those directly. Solution: mark the dataset as AFNI-format, after
loading it and before changing its name.
* Modified Makefile.* to use a 'MAKE' macro instead of the fixed 'make'
command.
13 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_dicom.c to alter operation of AFNI_SLICE_SPACING_IS_GA
P
so that 'NO' means use the Spacing attribute even if it is smaller than
the Thickness attribute. Seems to be needed for Phillips.
12 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to draw graymap in histogram style. Also added
'ent=' entropy value to numerical range display.
10 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mrilib.h, mri_read.c, and to3d.c to allow use of inter-slice
spacing to override slice thickness, at least for GE I.* files.
08 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifications to mcw_malloc.c to print out traceback chain when
corruption is detected.
* Added ENTRY()/RETURN() to a number of mri_*.c functions.
* Modified afni.c to display surface overlay from other datasets in
the same directory, if the current underlay datasets doesn't have
any surfaces.
07 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifications to plugins and models to make them work with g++.
02 Jan 2004, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* More annoying bugs in NIML stream I/O. Also, when a socket is
closed, send 1 byte of OOB data so that the receiving process
will receive SIGURG. The new SIGURG handler will then shut
the socket down on the other end, without the user having to
read the 'close_this' element.
30 Dec 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed annoying bugs in NIML stream I/O.
* Modified niml/niml_do.c to allow user to register callbacks that
supplement builtin verbs.
23 Dec 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Checked in many changes to deal with compilation of afni with g++
(version 3.2 or later).
17 Dec 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed Amalloc.h bug.
16 Dec 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to niml/ functions to make them g++ compatible.
* Added 'r/R' to imseq.[ch] and afni_graph.[ch].
07 Dec 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified ts.c to allow '#' comments in RWC_read_time_series().
05 Dec 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Some tweaks to mpegtoppm and mri_read_mpeg.
* Fixed bug in niml/niml_element.c -- NI_free_element() would fail if
nel->vec was NULL.
* Similar problem in thd_3Ddset.c.
04 Dec 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Change 'm/M' to 'v/V', and also add to afni_graph.c.
03 Dec 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Program mpegtoppm -- in mpegtoppm_dir/.
* Read images and datasets from MPEG files, via mpegtoppm.
* 'm' and 'M' keys in imseq.c.
01 Dec 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to add AFNI_IMAGE_ZEROCOLOR environment variable.
* Modified mcw_glob.[ch] to add simple-to-use function MCW_wildcards().
Used this in afni_splash.c as a test.
01 Dec 2003, RC Reynolds, SurfMeasures, level 3 (MAJOR), type 1 (NEW_PROG)
program to compute various measures over surfaces
24 Nov 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fun with Apple's speech synthesis.
21 Nov 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added ability to undo Linear Fillin to plug_drawdset.c.
20 Nov 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in arrowpad movement, in afni.c: must do LOAD_DSET_VIEWS(im3d)
.
* Modified afni.c and afni_version.c to write UPDATER script, if possible.
19 Nov 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Multiple level undo/redo in plug_drawdset.c.
18 Nov 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to prevent beep when user tries to zoom when Mont
is on, or vice-versa.
14 Nov 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* More minor changes to 3dcalc.c and parser.f for slight speedups.
13 Nov 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added argmax() and argnum() functions to parser.f and 3dcalc.c.
* Modified Makefile.solaris28_suncc per Vince Hradil's experience.
* Split up load vector loops in PAREVEC() in parser.c, for speed.
05 Nov 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to auto-popdown graymap plot if it was auto-popupped
in the first place.
* Also added 'Edit Environment' button to image window popup menu.
04 Nov 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to move crosshair focus on Button1 release, rather than
press. This makes the graylevel change via Button1 motion not have
the annoying focus change side effect.
* Modified afni.c, etc., to implement new environment variables
AFNI_IMAGE_MINTOMAX and AFNI_IMAGE_GLOBALRANGE.
* Modified afni_plugin.[ch] to allow plugins to change the 'Run' button
labels to something else.
30 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Some changes (f2cdir/ and afni_plugin.c) for Mac OS X 10.3 compilation.
29 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Allow '# ' as a comment in .afnirc -- changes to afni_setup.c GETSTR mac
ro.
28 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to thd_automask.c and 3dAutomask.c to implement -eclip option.
27 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Auto-popup and auto-place graymap plot.
* Change plug_drawdset.c to disable auto-popup of graymap plot when plugin
is open, and re-enable it when plugin closes.
24 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Graymap Plot' to imseq.c.
23 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified Button1 in intensity bar to always do re-aspect, even if free
aspect is on.
* Added Button1 stroke right/left in image window to change contrast and
brightness together; changes to imseq.[ch], display.[ch], and
afni_pplug_env.c.
22 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Inten->Save Palette with colorscales now saves a colorscale file.
* Inten->Read Palette with colorscales now reads a colorscale file.
* AFNI_MPEG_FRAMERATE in imseq.c.
* Extend short input time series in 3dDeconvolve.c.
21 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added label popup menu to Draw Dataset plugin.
* Added Button1 click in intensity bar to re-aspect image window.
Also, skip attempt to reconfigure if happened before within last 33 ms.
This is to avoid getting into fights with the window manager.
20 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed scaling bug in mri_warp3D.c -- datasets with scaling factors were
being scaled before warp, but not unscaled after warp, so that the
surviving scale factor would be applied twice.
* Added labelizing to Draw Dataset plugin.
15 Oct 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added poetry.
* Removed 'points'.
* Added Dtables to niml.
28 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Widespread changes, including addition of thd_niftiread.c, to read
NIFTI-1 formatted files as datasets.
* Modified afni.c to read datasets individually from command line argv's
if they can't be read as sessions.
26 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to skip printing adoption warnings unless user
explicitly requests them with an environment variable.
24 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dLRflip.c to give output dataset a new prefix (oops).
23 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added AFNI_MAX_OPTMENU environment variable (bbox.c, etc.).
* Modified Makefile.INCLUDE to chmog ugo+x the ./configure files
in a couple of subdirectories.
15 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -version option to afni.c, per Rick Reynolds.
11 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in afni_sumafunc.c, where func threshold image is bytes -- was
using index ar_thr[ii] instead of ar_thr[jj] -- not good.
08 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Problem: when anat_now == fim_now, and fim_now got set to
'Warp Func on Demand', then trouble. Solutions
- make AFNI_VIEW_FUNC_BRICK and AFNI_VIEW_ANAT_BRICK default to YES.
- make sure if anat_now == fim_now, Func WOD is turned off.
07 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed small typo in index in mri_warp3D.c quintic code.
* Fixed CYGWIN bracket placement at end of thd_loaddblk.c.
06 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Somehow, a bug crept into the Read Session function (in afni_func.c) tha
t
rejected new sessions with # datasets > 0 rather than # datasets == 0.
* Added quintic interpolation to mri_warp3D.c, and 3dWarp.c.
* Added -fsl_matvec option to 3dWarp.c.
* plug_3ddup.c created (but not part of the binaries, yet).
05 Aug 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_1Ddset.c to read a multi-column .1D file as a 3D+time datas
et
rather than a bucket, if AFNI_1D_TIME is set to YES.
* Modified mri_write_ascii() to write the stdout if the filename is '-'.
* Modified various *.c files to avoid warning messages on OS X compiles.
05 Aug 2003, RC Reynolds, 3dVol2Surf, level 4 (SUPER), type 1 (NEW_PROG)
program to map data from the volume to domain to the surface domain
30 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_nudge.c to add NN interpolation option.
* Modified THD_open_3dcalc() to make dataset directory './' after it is in
put,
so that EDIT_empty_copy() of it will not put new dataset into /tmp.
* Modified afni_func.c and afni_sumafunc.c to threshold byte and short
overlays in float rather than int.
* Modified FUNC_IS_STAT() and FUNC_HAVE_PVAL() macros in 3ddata.h to retur
n 1
only if the code supplied corresponds to a valid statistic code.
* Various fixes to the anat/func interchangeability stuff.
29 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Many many changes to make func and anat datasets work interchangeably in
the interactive AFNI.
* 3dmerge.c now has -verb option.
28 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dcalc.c to force scaling for short and byte output datum when
non-integer values are found in the dataset.
23 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to thd_info.c to print more than 8000 characters from the Histor
y.
* Changes to thd_notes.c to make Addto_History work right.
* Changes to 3dcalc.c to use Addto_History correctly.
22 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* More expansion in parser.f, etc.
* Modified coxplot/plot_ts.c and 1dplot.c to let user control x- and y-axe
s
in more detail.
21 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified all uses of XmCreatePopupMenu() to make parent widget different
than
the Button-3 popup widget when using Solaris -- some bug in Solaris see
ms to
cause a popup problem when the parent of the menu is also the one getti
ng
the ButtonPress event.
* Modified afni_graph.c, imseq.c, afni.c, plug_nth_dataset.c, etc., to hav
e
the Dataset#N, Dataset#2, and Expr0D plugin windows open when these
transformations are selected from menus.
* Modified the parser to take longer expressions.
18 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifed imseq.[ch] (etc.) to include a 'pen' box to turn on the 'pen dra
wing'
Button-1 mode (only available when drawing has been enabled).
15 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Included FreeBSD patches from Jason Bacon.
10 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in afni_graph.c of colors in dplots from Dataset#N plugin.
06 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dmaskave.c to add -median option.
03 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added ISQ_snapsave() to imseq.c, which lets the user supply the image to
be
saved in a snapshot, rather than acquire it from a widget like ISQ_snap
shot().
01 Jul 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to change pbar hints when 'Func=Threshold' is press
ed.
* Added RWC_XtPopdown() to xutil.[ch], and modified most code to use this
rather than XtPopdown().
* Added empty XtErrorHandler to afni.c to try to avoid crashes when an Xt
error occurs.
* Added mri_equal.c, which checks if 2 images are equal. Used in ISQ_snap
shot()
to avoid saving duplicate images in succession.
26 Jun 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Moved some snapshot stuff to xim.c rather than imseq.c.
* Modified afni.c to have it continue after fatal X11 errors.
* New program 1ddot.c.
25 Jun 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* ISQ_snapfile(Widget) added to imseq.c; other tweaks to ISQ_snapshot().
20 Jun 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to add ISQ_snapshot(Widget) functionality. Tested
in Xphace program.
* Modified Makefile.INCLUDE to make libmrix.a that includes all the
X11 utilities (imseq.c, xutil.c, xim.c, etc.).
16 Jun 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* SUMA+AFNI ROI stuff.
13 Jun 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to prevent resized windows from getting bigger than
AFNI_IMAGE_MAXFRAC (default=0.9) times the screen dimensions.
* Modified niml/niml_elemio.c to make attribute string buffer size expand
when Ziad writes huge attributes, the fiend. Also put a newline before
each attribute, whether we want it or not.
11 Jun 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c NOT to call AFNI_set_thresh_top() in AFNI_setup_viewing(
)
when changing functional datasets.
06 Jun 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified niml/niml_stream.c to disable reopen of tcp: stream as shm: if
AFNI_NOSHM environment is set to YES.
29 May 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dttest.c to output t-statistic brick in floats if diff brick i
s
stored as floats.
* Modified 3dcalc.c to floatize datasets that don't have constant sub-bric
k
datum.
* Per the request of Ziad Saad, added function NI_add_column_stride() to
niml/niml_element.c.
29 May 2003, RC Reynolds, 3dSurf2Vol, level 4 (SUPER), type 1 (NEW_PROG)
program to map data from the surface domain to the volume domain
14 May 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in thd_intlist.c, where ']' or '}' might not stop the scanning
of
the string. This was a problem when dealing with inputs that have both
types of selectors -- one might run over another in the parsing.
13 May 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added '-Fourier_nopad' option to 3drotate.c, plug_nudge.c, and thd_rot3d
.c.
* Modified afni.c to have arrowpad keys do wraparound when they hit the ed
ge.
12 May 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_initdkptr.c to have prefixes that start with '/' override a
ny
input directory name.
* Modified waver to allow 'a:b' and 'a%c' durations for '-tstim' input.
09 May 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* AFNI_THRESH_BIGSTEP environment variable.
* Boxes in 3dmaskdump.c.
07 May 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Parallel computation (-jobs option) addtions to 3dNLfim.c.
* Mods to mri_dicom_hdr.c to subtract 1 from rwc_err for each error messag
e.
This way, will normally only print 1 such message per to3d run, which w
ill
make the users happier, I hope.
* Add mri_possibly_dicom() function to mri_read_dicom.c, and use it to cen
sor
which files get the full DICOM reading treatment.
06 May 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Minor changes to 3dDeconvolve.c.
* From Rich Hammett, AFNI_TRY_DICOM_LAST environment variable.
04 May 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Parallel computation (-jobs option) addtions to 3dDeconvolve.c.
01 May 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified NLfit.c and plug_nlfit.c to have NLfit_error() be able to use l
ongjmp()
to deal with errors, rather than exit().
* Modified afni_func.c to rotate color bar in steps of 4 if Shift key is p
ressed.
30 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_intlist.c to let '{}' bound the list as well as '[]'.
* Modifed mri_read_1D() to use intlist of the form '{..}' to do row sub-se
lection,
as well as the older '[..]' for column sub-selection.
* Modified most programs that used mri_read_ascii() to read timeseries fil
es to
use mri_read_1D() instead, so that the '{..}' feature can be supported.
29 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c and machdep.h to add ENFORCE_ASPECT #define (for Mac OS
X).
28 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dcalc to add -taxis option.
* Added mri_fromstring.c, to input 1D data in the form '1D:5@0,10@1,5@0',
etc.
24 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dTshift.c and thd_tshift.c to negate time shift, since it seem
s have
been wrong all these years.
22 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dTagalign.c (and thd_shear3d.c) heavily to use THD_warp3D() in
stead
of rotation-only functions, and to allow different kinds of transformat
ion
matrices to be used.
18 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program 3dWarp.c (along with mri_warp3D.c).
* Minor changes to 3dAnhist.c for Lukas Pezawas.
16 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dUniformize.c to allow byte-valued datasets, and added to stan
dard
distributions. Also modified estpdf3.c and pdf.c to obey the global
'quiet' variable, if the USE_QUIET macro is defined.
15 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in mri_overlay.c (using data from imover instead of imov!).
12 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified waver.c -tstim option to skip argv[]'s that start with whitespa
ce
-- this is to deal with evil Microsoft CR-LF line breaks.
11 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot/plot_ts.c to allow setting of line colors using
AFNI_1DPLOT_COLOR_xx environment variables.
09 Apr 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed thd_shear3d.h function DMAT_svdrot() to work properly when input m
atrix
is singular.
29 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_resize() [in mri_warp.c] to properly deal with images of
MRI_byte, MRI_short, and MRI_rgb types.
28 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to afni_splash.[ch] to include faces!
27 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified NIML to allow ni_dimen=0 on input, and then infer length of vec
tors
from input data.
23 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -xyz option to 3dmaskdump.c.
21 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added thd_3Ddset.c to read AFNI datasets from NIML-formatted
.3D files. Corresponding changes to 3ddata.h, etc.
* Changes from Doug Ward
1) Program 3dDeconvolve: Added -quiet option to suppress screen output
.
2) Plugin Deconvolve: Additional input error protection for -censor an
d
-concat options. These options could cause afni to crash if the input
files were not set up correctly.
3) Program RSFgen: Added -table option, to generate random permutation
s of
the rows of an input column or table of numbers. Useful for randomiza
tion
studies of statistical thresholds, about which more later.
4) Libraries matrix.c and matrix_f.c: The recently added/modified matr
ix
routines vector_multiply and vector_multiply_subtract would produce a
segmentation fault for certain input matrices (e.g., null baseline mod
el).
This has now been corrected (hopefully).
20 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c, 3ddata.h, afni_graph.c to allow graphing of
datasets with only 1 point along a spatial dimension (i.e., '.1D'
files).
* Modified niml/elemio.c to allow writing and reading of elements
with the '# ...' line format for header/trailer fields. Also
modified thd_1Ddset.c to write .1D dataset files out in this
format.
19 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dAFNItoANALYZE.c to add -orient option.
* Added mri_flip3D.c to flip 3D images around.
* Added thd_getorient.c to get axis direction in a dataset for
a given orientation code.
* Modified mri_copy.c to work if input image doesn't have data array.
* Added environment variable AFNI_MINC_SLICESCALE to thd_mincread.c.
* Fixed bug in thd_mincread.c in slice-scaling when datum is floats
(subtracted intop instead of inbot in scaling formula).
* Modified thd_mincread.c to downscale short or byte datasets if
slice scaling would push them past the maxval for that data type.
Also, use calloc() on im_min and im_max arrays to avoid problems
when those arrays in the MINC file are incomplete.
* Modified 3drefit.c, and thd_delete.c to skip CTF and 1D files.
* Modified 3drotate.c to skip rotation if rotation matrix is identity.
Also modified 3dvolreg.c and 3drotate.c to use '%.4f' format when
writing command string to THD_rotcom_to_matvec().
18 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed 1dplot.c -stdin option to work again (oops).
14 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* A few more changes to 3dAnhist.c.
* Modified thd_opendset.c to also deal with .1D inputs.
13 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to 3dAnhist to regress histogram and plot it.
* Changes to coxplot/plot_ts.c to have it avoid 'pushing' data limits out.
* Changes to 1dplot.c: -xzero and -nopush options.
* Added THD_generic_detrend() to thd_detrend.c, and used this to add a
-ort option to 3dTcorrelate.
* Modified thd_notes.c and 3dNotes.c to avoid escaping the '\' character
for notes input from the command line.
11 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified tagset.h to increase number of allowed tags.
10 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.[ch] to make F2 button have Button1 operate as Button2,
and to show cursor as a pencil shape for drawing when this mode is on.
07 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program 3dAnhist.c.
06 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dWinsor.c to use -mask option.
05 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a bug in AFNI_setup_viewing() that crept in - assumed existence
of fim_now, which might not be true.
* Incorporated fix of mri_read_dicom.c from Rich Hammett, to skip false
targets in the Siemens extra info. (Will no one rid me of this
troublesome mosaic format?)
* Modified 1dplot.c to accept multiple timeseries file inputs.
* Modified thd_automask.c to have a mri_automask() function as well.
* Modified 3dAutomask.c to do fillin and exterior-clipping if -dilate
option is used.
04 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to get rid of bug when de-sensitizing thr_rowcol for RGB
images. Now it is always sensitized. Also, afni_func.c now will deal
with RGB images as thresholds (just converts them to floats, though).
* Added thd_1Dtodset.c, functions to read and write 1D files as AFNI datas
ets.
* Added niml/niml_stat.c to be a place to store statistics code for NIML.
03 Mar 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Created matrix_f.[ch] as float alternatives to matrix.[ch]. Then used t
his
in 3dDeconvolve.c and RegAna.c to create a program 3dDeconvolve_f compi
led
from 3dDeconvolve.c when the FLOATIZE C macro is defined. Speedup on a
Linux box is about 40% (due to less memory fetch).
* Modified mri_read_dicom.c to allow user to skip stupid GE fixup entirely
.
28 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Per Lukas Pezawas of CBDB, modified 1dgrayplot.c to have -ps option,
like 1dplot.c. While doing so, also fixed a bug in coxplot/plot_ps2.c
where the rectangle case didn't have a 'break', so fell through and
drew a circle as well.
* Modified mritopgm.c to have a clipping option.
27 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve.c to get multiple timeseries at once, to reduce
cache thrashing.
* Modified thd_notes.c to add function to append one dataset's history
to another's. Used this in 3dcalc.c as a starter.
26 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.c and afni_sumafunc.c to allow drawing of triangle
intersections at edges of slice plane, as well as at center.
* Modified 'view_setter' code to work more intuitively when only one
image viewer is open, etc.
24 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to draw a * in the box of the closest surface node.
* Modified 3dhistog.c to print '#' at start of header lines, so that
result can be read by mri_read_1D(), etc.
* Incorporated changes from KRH to fix mri_read_dicom.c for Siemens
mosaics with incomplete slice coordinates.
* Modified afni_graph.c to fix problem with double plot introduced
when multiple timeseries graphing was introduced - forgot to
reset tsar pointer to original data when graphing double plot
in plus/minus mode.
23 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.[ch] and afni_sumafunc.c to create boxsize and linewidth
controls on the 'Control Surface' popup.
* Modified coxplot/plot_x11.c to flip line segments if that will make
them join. Also, initialize thickness of plots to 0, to allow for
special case (circle, box, ...) that is first item plotted.
21 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to use '-bpp 24' in ppmtobmp output to BMP files, avoid
ing
quantization problems.
* Modified afni.c to add a '#NodeID' string to the Button-3 image viewer p
opup,
when a surface is present.
20 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to imseq.c, afni.[ch], afni_receive.c, and plug_drawdset.c to ma
ke
the keypad 'Delete' key(s) operate like the Undo button in the drawing
plugin.
* Modified afni_receive.c to have a string name debug output for each
receive callback (and all the functions that call this). Also fixed a
bug that would have functions registered for different receive cases
get inappropriate calls (forgot to enclose the call in {..} in an if).
* Modified afni_suma*.c to send closest surface node ID to SUMA when viewp
oint
change callback is invoked.
19 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a couple little points in niml_rowtype.c.
* Modified afni_sumafunc.c (afni.h, etc.) to change 'Control Surface'
label for each surface into a toggle button, to make it easier to
turn surface on and off quickly.
18 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to add a hint to the colorscale.
* Modified NIML stuff to use rowtypes more properly (niml_element.c, etc.)
.
* Modified various Makefile.* to define SHOWOFF macro (once again).
* Modified afni_version.c to print out appropriate wget command for update
.
* Modified afni.c to printout precompiled version, if present.
12 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified niml/ to read/write full type names rather than just abbreviati
ons
to the 'ni_type' attribute of data elements.
* Modified niml/niml_do.c to add a 'typedef' verb, and to let the user pro
gram
define its own verb/callback pairs.
* Modified afni_niml.c to define a 'ni_do' verb 'DRIVE_AFNI', to let exter
nal
program (hint: SUMA) access this stuff.
11 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dfractionize.c to set default clip value to a very tiny positi
ve
value, rather than 0.
* Modified pbar.[ch] to use a popup menu to deal with Button-3 events, rat
her
than directly do stuff. Included a value+color label on this menu.
10 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.[ch] and afni.c to allow initializing graph matrix s
ize
to value other than 3, through AFNI_graph_matrix environment variable.
* Modified 3dcalc.c to allow RGB dataset input.
06 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* This time, modified 3ddata.h, afni.c, afni_func.c to ALWAYS keep thresho
ld
slider active, and when there is no threshold, use the function for the
threshold. (However, RGB overlays are not thresholded, so this is the
only case in which the threshold slider is desensitized. Also, the fir
st
time the user switches to a fim dataset, the threshold slider is set to
0.)
* Modified to3d.c to deal with double input images (to be converted to flo
ats).
Also changed mri_read.c, mcw_glob.c, mri_swapbytes.c, 3ddata.h to add
a '3Dd:' input format for reading doubles from arbitrary files.
* Added some new default colorscales to pbar.c.
05 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'OPEN_PANEL' command to afni_driver.c, and to afni_splash.c.
04 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Moved user-defined colorscale setup to pbar.c from afni.c.
* In afni_widg.c, use AFNI_COLORSCALE_DEFAULT to setup initial colorscale.
03 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to afni_driver.c to support colorscales.
* Saving .afni.startup_script now also saves the Autorange/funcrange setti
ng.
02 Feb 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_sumafunc.c to use 'big' mode colorscales.
* Modified afni.c, pbar.c (etc.) to read in user-defined colorscales
from files.
31 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to de-sensitize threshold slider when not needed, rather
than hide it. This is to get around a problem with the size of the pba
r
being adjusted slightly incorrectly, for reasonse I don't understand.
* Modified pbar.c to give choice of colormaps for 'big' mode. Programmed
a startup set of 4 colormaps.
30 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified pbar.c, afni_func.c, etc., to add a 'big' mode to the pbar, wit
h
128 colors. More work is needed here for SUMA, rendering, scripting,
loading colormaps, etc.
29 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3drefit.t to add -Torg option (for MEG guys).
28 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_ctfread.c to correct nx,ny,nz calculation for SAM images.
* Modified afni.c to do the time lock properly when the anat has no
time axis but the func does.
* Modified 3dcopy.c to work with copying non-AFNI datasets.
27 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added messages to afni_version.c when version checking is disabled, fail
s,
or when the current version is different than the last version.
24 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added special function key stuff to imseq.c (arrows, PgUp/PgDn).
23 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Made AFNI_VALUE_LABEL default be YES instead of NO.
* Added AFNI_DEFAULT_OPACITY environment variable, for image overlay opaci
ty.
* Added AFNI_DEFAULT_IMSAVE environment variable, for .jpg, .tif, etc.
* Fixed bug in afni_driver.c SETENV function - space used for putenv() mus
t
be permanent memory, not temporary!
22 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Run Script' button to Datamode->Misc menu.
* Made 'Save Layout' button save setup script to .afni.startup_script
if no filename is entered.
21 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* More additions to afni_driver.c.
* Changes to afni.[ch] to allow startup script to drive AFNI setup.
16 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to let user setenv AFNI_AGIF_DELAY to control speed
of animated GIF output.
* Modified afni_driver.c to allow remote changing of thresholds, the
addition of overlay colors, and the setting of pbar pane number.
15 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to let user set SUMA line thickness via environment
variable. Also changed afni_pplug_env.c to match.
* Modified afni_func.c to purge all datasets in a session after rescan.
15 Jan 2003, RC Reynolds, Imon, level 3 (MAJOR), type 2 (NEW_OPT)
added connection to the realtime plugin in afni
10 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified edt_blur.c to clip output to input range.
02 Jan 2003, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added a error message to mcw_malloc.c to note when an allocation fails.
31 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified niml/niml_rowtype.c to deal with String type and debugged
stuff with output of var dim arrays.
30 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Minor change to AFNI_rescan_session() users to print out number of
new datasets rows.
29 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Minor change to afni_version.c to print out 'Latest News' web page
when version comparison fails.
28 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified AFNI_rescan_session() in afni_func.c to NOT clobber existing
dataset pointers when adding datasets to a session.
* Removed all instances of OMIT_DATASET_IDCODES.
27 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dttest.c to save DOF dataset if -unpooled is used.
24 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_dicom.c to save Siemens extra info string even if
file isn't a mosaic.
23 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_dicom.c to correct error in z-axis orientation from
multiple 1-slice datasets - code had been copied from mri_read.c, but
that was for GE LPI coords, and DICOM is RAI.
* Modified mri_read_dicom.c to use Rescale and Window tags, if turned on
by the relevant environment variables.
* Modified aiv.c to use globbing on input filenames.
20 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified niml/niml_do.c to add verb 'close_this' to close a stream.
This is to let a stream be closed from the other end.
* Modified niml/niml_stream.c to send a 'close_this' message when
a tcp: or shm: stream is closed.
* Modified niml/niml_stream.c to mark NI_stream's for 'death' in
NI_stream_close_keep(), and then avoid using such streams in
other functions. This is to let a stream be closed without
freeing its struct.
19 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added THD_mkdir(), THD_is_ondisk(), THD_cwd() to thd_filestuff.c.
* Modified afni_driver.c to add commands SYSTEM and CHDIR, which call
system() and chdir() [pretty clever names, huh?]. Also modified
afni_driver.c to trim trailing blanks from the input command
before passing it to the handler functions.
18 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_realtime.c to add ZGAP and XYZOFF features from Larry Fran
k.
* Fixed bug in niml/niml_util.c decode_string_list() function where
the sar->str array was allocated with sizeof(char)*num rather than
sizeof(char *)*num. Not good in the long run.
* Modified niml/niml_rowtype.c to allow rowtypes to have 1D variable dimen
sion
arrays.
16 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Moved niml.[ch] into niml/ subdirectory, and modified Makefile.INCLUDE
accordingly.
12 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_niml.c and afni_sumafunc.c to create functional
colormaps for all surfaces on the anat dataset, not just the
first surface. Also fixed it so that fim=0 is not overlaid.
* Modified thd_iochan.c to use IOCHAN_DELAY_RMID environment variable
to indicate that deletion of shm segments should only occur when
no one is attached to them. This is to get around a problem on
some Unices.
* Modified Makefile.INCLUDE rule for cjpeg to remove old Makefile and
jconfig.h, since these are re-made by the configure script.
* Modified niml.c to shmdt() before shmctl(IPC_RMID) instead of after.
* Modified afni.c to skip version check if realtime is on. Also modified
afni_version.c to add an atexit() handler to delete the child-parent
shared memory IOCHAN when the program exit()'s.
* Modified rtfeedme.c to add a signal handler to close the data IOCHAN
if the program crashes.
11 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_realtime.c to allow termination of a dataset without
closing the data IOCHAN. Also added new XYZFIRST metadata command,
to allow setting of all 3 axis offsets.
* Modified rtfeedme.c to test the above features.
09 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to save temporary files for animated GIF or MPEG
output with a random suffix, to avoid collisions if 2 copies
of AFNI (or aiv) are running.
* Modified niml.[ch] to allow definiton of 'NI_rowtypes' to make it easier
to deal with structs (with all fixed length elements, alas).
* Modified nids.[ch] to deal with vectors of arbitrary NI_rowtype.
07 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to change image number on '<' or '>' keys (like
the graph windows).
05 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added CTF SAM file input to thd_ctfread.c.
* Modified 3dIntracranial.c to convert input dataset to shorts if it is
stored as bytes. The output will still be shorts.
04 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added thd_ctfread.c to read CTF MRI files as datasets.
* Modified thd_initsess.s, thd_opendset.c, thd_loaddblk.c, 3ddata.h to
use the CTF functions.
03 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified niml.c to use setsockopt() to change socket buffer sizes only
if getsockopt() says they are too small.
02 Dec 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_crender.c to use mcw_graf.c stuff of 30,NOV,2002.
* Modified mri_read_dicom.c to deal with Siemens Mosaic differently, to
accomodate variations from NYU's Allegra scanner (vs. NIDA's).
* Modified to3d.c to show NX x NY along with Datum in GUI.
30 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mcw_graf.[ch] to draw a coordinate label during drag of graf
handle with Button 3.
* Modified mri_read_dicom.c to deal with GE's incorrect use of Slice Spaci
ng
as gap, rather than center-to-center distance. Ugh.
29 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_stuff.c to allow for case when initial 4096 byte buffe
r
contains all the image data (i.e., for tiny images).
* Modified coxplot/plot_ps.c to allow output to stdout.
* Modified 1dplot.c to allout PostScript output to stdout.
27 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_dicom.c to allow for stupid GE case where slice spacin
g is
incorrectly set to slice gap instead.
27 Nov 2002, RC Reynolds, Imon, level 4 (SUPER), type 1 (NEW_PROG)
program to monitor GE I-files as they are written to the scanner
25 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_friends.c to add date-based trivia (also, afni.[ch]).
23 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_version.c to only do a check once every 12 hours.
22 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added mri_read_stuff.c to filter input from JPEGs, TIFFs, BMPs, etc., in
to
mri_read.c.
* Added afni_version.c to check AFNI version at startup.
* Modified edt_dsetitems.c to strip '+orig' etc. from tail of new prefix.
21 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added some extra programs (gifsicle, mpeg_encode, cjpeg, etc.) to the PR
OGRAMS
macro in Makefile.INCLUDE.
18 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified niml.[ch] to make the NI_malloc() package use tracking function
s,
which I stole from mcw_malloc.c - of course, I wrote that, too, so 'sto
le'
may be too strong a verb.
13 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_splash.[ch] to allow color top overlays. Incorporated SSC
C group
picture.
12 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changed MAX_CONTROLLERS in afni.h for Mike Beauchamp.
05 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program rotcom.c, to print out matrix+vector from '-rotate ... -as
hift ...'
options that would be input to 3drotate.
* Fixed mri_read.c, mri_read_dicom.c, mri_dicom_hdr.c to stop annoying pri
ntout of
messages about bad DICOM files when trying to read GE I.* files.
04 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added MRI_rgb type to thd_zeropad.c and to BRICK_*_MASK macros in afni_p
lugin.h.
* Took changes from Rasmus Birn to add a '-gamd' delay option to waver.c.
01 Nov 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* More changes for mosaic input.
28 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to mri_dicom_hdr.c and mri_read_dicom.c to deal with Siemens' st
upid
mosaic format.
25 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_drawdset.c to use sorting to prevent vast numbers of dupli
cates
when inserting large R circles/spheres.
17 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_drawdset.c sphere/circle insertion not to test for duplica
te
insertions from the 1st input point - this speeds things up for large R
.
16 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_drawdset.c to add '2D Circle' and '3D Sphere' drawing mode
s.
10 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_analyzeread.c to correct signs of origin when orientation h
as
some negative axes.
08 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_drawdset.c (and imseq.[ch], afni_receive.c, afni.h) to mak
e
button2 drawing overlay have thicker lines, closer to what will actuall
y
be filled. Also added 1 larger '3D Nbhd' stencil.
07 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_drawdset.c to add '2D Nbhd' and '3D Nbhd' drawing modes.
* Also rearranged the Copy and Choose Dataset buttons.
04 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Took modified plug_deconvolve.c from Doug Ward, to fix bug when baseline
is disabled.
* Modified thd_analyzeread.c to add AFNI_ANALYZE_AUTOCENTER option.
* Modified 3drefit.c to add -xorigin_raw (etc.) options.
* Modified thd_intlist.c to skip blanks in the [] sub-brick selector strin
g.
03 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to allow use of Shift+Button1 for drawing as well as
Button2. Changes also to afni_graph.c and plug_drawdset.c (the
latter just to change the help text).
* Modified 3dTcat.c to use last '+' as marker for '+orig' (etc.)
rather than 1st.
01 Oct 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_realtime.c to allow input of notes via a NOTE command.
Also modified rtfeedme.c with -note option to test this out.
01 Oct 2002, RC Reynolds, file_tool, level 4 (SUPER), type 1 (NEW_PROG)
program to perform generic manipulations of binary files
30 Sep 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dAFNItoANALYZE.c (and mri_write_analyze.c) to allow output of
AFNI datasets into a 4D ANALYZE format file.
10 Sep 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_dicom.c to print out at most 9 warning messages of
each type.
* Modified to3d.c to open X11 immediately when -nosave is used. Also adde
d
a bunch of ENTRY/RETURNs to ferret out a bug (it's still hidden).
* Oops. Forgot to fclose() the fopen()-ed file in mri_read_dicom.c. This
was causing the problems in to3d mentioned above.
* New program dicom_to_raw.c.
09 Sep 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* ISHEADTYPE macro in 3ddata.h used '=' instead of '=='; this was bad.
* 'Q' and 'q' quits in afni_widg.c and afni_func.c (hidden_EV).
04 Sep 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* More cosmetic changes to 3dDespike.c.
03 Sep 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify 3dDespike.c to allow float datasets, print nicer messages, etc.
* Fix my_tanh() bug in 3dDespike.c, which was returning NaN for very
large inputs.
01 Sep 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Program 3dDespike.c, to patch a problem with the 3T-1 scanner.
28 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_initsess.c and thd_analyzeread.c to support FSL/FEAT
input .map files.
27 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read*_analyze() functions to always floatize ANALYZE
data if the SPM funused1 scale factor is present.
* Added ANALYZE (thd_analyzeread.c) file input to datasets.
26 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added Htable (string/pointer pair) hash table functions to niml.[ch].
* Added mri_read3D_analyze75() to mri_read.c, to read an ANALYZE file
as an array of 3D images, rather than 2D images.
23 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_loaddblk.c to print (stderr) a message when loading a
large dataset.
* Modified niml.[ch] to implement NI_reopen_stream() and make a first
cut at NI_do().
21 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified niml.c to add NI_mktemp(), and change use of /dev/urandom.
* Modified machdep.c to change use of mallopt() for Linux - seems to
make big malloc()'s work better (?).
* Modified thd_fetchdset.c to use niml.c functions, instead of the
older thd_http.c functions.
20 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifications to surface controls: hints, help, comments.
* Added UUID functions to niml.[ch].
19 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_sumafunc.c (afni.h, etc.) to have a control panel for
surface stuff. At this time, lets user set colors.
16 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.[ch] and afni.c to suppress multiple image redraws
when an image window is first opened.
* Modified plug_nudge.c to extend range of angle and shift choosers.
* Modified xutil.h WAIT_for_window() macro to wait a little longer.
This is in an attempt to get rid of random problems with graph
windows opening with bad Pixmap contents.
14 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified various things (afni.h, afni.c, afni_niml.c, afni_suma.c)
to allow for multiple surfaces per dataset.
* Modified niml.h to disable shm stuff for Cygwin.
13 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to destroy dialog widget before imseq top widget.
* Fixed array overflow by 1 bug in mri_percents.c.
* Modified mri_read.c to check for .hdr files before DICOM.
* Modified 3dToutcount.c to save result as a FIM, and to save history.
08 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added color save/load to afni_ttren.c.
07 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed cl1.c and incorporated into libmri.a.
* Added plugin plug_L1fit.c to provide a L1 analog to plug_lsqfit.c.
* Modified 3dToutcount.c to use cl1_solve to remove trends before
outlier-ing.
06 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_driver.c to allow 'iconify' option on OPEN_WINDOW commands
.
* Modified afni_driver.c to return controller index only if the input
string is only 1 character long or the 2nd character is a '.'.
* Modified afni_func.c and bbox.c to deal with potential strlist[] overflo
w
problems.
05 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Removed DEBUGTHISFILE macro from all places that used it.
* Modified plug_realtime.c to deal with case when more channels than
controllers are in use.
02 Aug 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_realtime.c to deal with multiple input channels.
* Modified rtfeedme.c to send multiple dataset channels.
31 Jul 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New function EDIT_wod_copy() to create a warp-on-demand copy, like 3ddup
.
* Use this in afni.c when a directory has only functions, no anats.
* Modified afni.c to allow -TRACE to work in realtime mode.
* Modified afni.c, afni_widg.c to make plugouts not crash during realtime
mode (we hope).
30 Jul 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_realtime.c to accept DRIVE_AFNI commands in the image prol
og.
* Modified afni.c to allow plugouts during realtime.
* Modified rtfeedme.c to send DRIVE_AFNI commands with the -drive option.
29 Jul 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified AFNI_read_images() in afni.c to use im->dx,dy,dz in '-im' usage
of program, if images read have voxel spacing (e.g., Analyze).
* Modified imseq.c to NOT turn off widgets if only 1 slice to display.
24 Jul 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified UNIQ_idcode() in niml.c to get 4 extra bytes from /dev/urandom,
if it is readable.
23 Jul 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_dicom.c to get slice orientation and offsets.
19 Jul 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New function mri_read_dicom() to read images from DICOM files.
15 Jul 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added mri_dicom_hdr.c and dicom_hdr.c - function and program to read/pri
nt
DICOM header info. Adapted from dcm_dump_file.c from RSNA, per the
suggestion of Jack Lancaster.
14 Jul 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Removed the dicomm<->surefit functions from Vecwarp.c since they are now
in libmri.a via afni_suma.c, and the Sun compiler doesn't like this.
05 Jul 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dmerge.c to prevent use of -keepthr on fim and fbuc datasets.
27 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified niml.c to add debugging output option (NIML_DEBUG).
* Fixed scan_for_angles() in niml.c to disable timeouts in case (b).
25 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified rtfeedme.c a little for debugging purposes.
* Modified thd_iochan.c to print better messages with PERROR().
* Modified plug_realtime.c to popup message when disk I/O is finished
after an acquisition ends.
24 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_analyze75() in mri_read.c to store funused1 scale
factor into dv MRI_IMAGE header field, for use in 3dANALYZEtoAFNI.c.
* Modified thd_writedset.c to allow re-writing of a VOLUMES dataset
.HEAD file.
* Modified plug_realtime.c to allow single slice dataset input (nzz=1).
21 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_info.c to print out disk storage mode of dataset.
* Started work on 3dANALYZEtoAFNI.c.
20 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_ascii() to catenate lines that end in '\', and do
some other minor stuff ('//' as a comment line, etc.).
* Modified thd_loaddblk.c (etc.) to support STORAGE_BY_VOLUMES.
20 Jun 2002, RC Reynolds, @make_stim_file, level 2 (MINOR), type 1 (NEW_PROG)
script to create binary stim files
19 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed clipping error in plot_cox.c (dangling else problem, d'oh).
17 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'crop' pushbutton to imseq.[ch].
* Modified default font for imseq to 7x13 in afni.c, and
modified imseq.c to shrink button margins, to squish widgets together.
14 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot/plot_x11.c to remove offset of 0.5 pixels from
line drawing code.
* Modified imseq.c to fix scaling of memplot overlays when cropping.
12 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.[ch] to add image cropping facility (Shift+Button2).
* Added function RWC_drag_rectangle() to xutil.c.
* Put MRI_COPY_AUX() into mri_cut.c (oops).
10 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.h and afni.c to incorporate RGBCYC cyclic color map from
Ziad Saad.
07 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Refined default threshold for termination of 3dvolreg.c.
06 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New programs 3dAutobox.c and 3dLRflip.c.
* New function mri_cut_3D() in mri_cut.c.
* Modified mri_3dalign.c to do trimming to save memory.
* Modified 3dvolreg.c to add -wtrim and -wtinp options.
06 Jun 2002, RC Reynolds, @SUMA_Make_Spec_FS, level 3 (MAJOR), type 1 (NEW_PROG)
script to import FreeSurfer surfaces into SUMA
04 Jun 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dAutomask.c to print out how many planes are cut off in the
the mask.
* Modified thd_automask.c to be faster.
31 May 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Adapted shm stuff from thd_iochan.c to niml.c.
28 May 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3drefit.c to add -clear_bstat option.
* Modified 3dAutomask.c to remove -fillin option.
* Modifed thd_automask.c to make fillin = brick size/60, and to make
final mask = complement of largest component of zeros.
21 May 2002, RC Reynolds, 3dresample, level 4 (SUPER), type 1 (NEW_PROG)
program to change a dataset orientation and/or grid spacing
17 May 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to allow image fraction change with 'i', 'I' keys.
14 May 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dZeropad.c to have -master option.
* Modified thd_zeropad.c to return full copy of dataset if input add/cut
values are all zero (used to return NULL).
11 May 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to put global session datasets into sessions as they
are read, rather than later - this allows the anats in the global
session to allow a session to be used, even if there are no funcs
in the directory.
07 May 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
Changes from Doug Ward
* The -one_col option has been added to program RSFgen. With this option,
the input stimulus functions are written as a single column of decimal
integers
(rather than multiple columns of binary numbers).
* The -stim_base option was added to Program 3dDeconvolve. This modificat
ion
allows the user to specify which input stimulus functions are to be inc
luded
as part of the baseline model. By default, the input stimulus function
s are
not included in the baseline model. This option will effect the output
values
for the Full Model R^2 and Full Model F-stat, since these statistics in
dicate
the significance of the full regression model relative to the baseline
model.
This option might be useful, for example, when the estimated motion par
ameters
are included as input stimulus functions. In most cases, the user woul
d want
the motion parameters to be part of the baseline model. By indicating
that
the motion parameters are part of the baseline model, they will not con
tribute
to the full regression model sum of squares.
* The Deconvolution plugin was also modified to incorporate the above chan
ge.
On the far right of each stimulus function input line of the Deconvolut
ion
plugin interface, there is a new option chooser labeled 'Base', which a
llows
the user to specify that this stimulus function is to be considered as
part of
the baseline model.
* The Deconvolution plugin was modified to allow a better graphical
representation of the estimated impulse response function when the user
selects
option DC_IRF under Tran 1D of the graph options menu. When using the
DC_IRF
function, note that the Double Plot option should be set to 'Off'.
* The 3dDeconvolve documentation was updated to reflect the above changes.
In particular, see Examples 1.4.3.2 and 2.3.2 of the Deconvolution manu
al in
file 3dDeconvolve.ps.
01 May 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Jump to (MNI)' button to image popup menu (afni_widg.c and afni.c
).
30 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dclust.c to add -mni option.
* Modified 3dclust.c, edt_clust.c, edt_clustarr.c, edt_onedset.c to allow
cluster rmm=0 to imply 6 NN clustering, vmul=0 to mean no volume editin
g,
and vmul<0 to mean min volume = fabs(vmul) voxels.
* Modified plug_drawdset.c to add 'Flood->Val/Zer' option. Also to turn
'See Function' on if the edited dataset is functional type.
* Added edt_clust2.c (NIH_find_clusters) to implement ISOVALUE_MODE and
ISOMERGE_MODE.
* Incorporated Ziad Saad's Ifile program into AFNI distribution.
29 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New functions in thd_mnicoords.c to translate TT atlas coords to/from
MNI template coords.
* Used above in thd_ttatlas_query.c.
* Samia Saad was born today!
28 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added the orientation changes to plug_render.c as well.
26 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* At last seem to have figured out how to make the orientations change
w.r.t. spatial axes - added these changes to plug_crender.c.
22 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified debugtrace.h to include 'last_status' variable: keeps of copy o
f the
last STATUS() string, and prints it when the program crashes.
* Modified thd_dsetdblk.c to deal with NULL dataset at very end - the SUMA
stuff
didn't check for that, which caused a crash if the dataset couldn't be
constructed.
19 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_automask.c to have fill in functions.
* Modified 3dAutomask.c to have -fillin option.
* Modified cox_render.c to remove memset() of new image to 0, since
mri_new() does this since 01,NOV,2001.
18 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_automask.c to erode/dilate the result, so as to clip off
tenuously connected blobs.
* Modified edt_clust.c to make MCW_erode_clusters() return void, not
void *, since it doesn't actually return anything.
17 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_sumafunc.c to allow for MRI_rgb fim overlays.
16 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_mincread.c to correctly use lower end of valid_range[].
* Modified thd_mincwrite.c to use '-range -scan_range' flags with
rawtominc program.
* Modified 3dvolreg.c and 3drotate.c to make -clipit the default.
* New program 3dThreetoRGB.c to create RGB datasets from 3 bricks.
* Modified mri_read.c to use new '3Dr:' input format for RGB files.
* Modified 3dAutomask.c to add history note.
* Modified afni_plugin.h and NLfit_model.h to read dlfcn.h from
dlcompat/ subdirectory on Darwin systems.
* Modified afni.c to allow environment variables to set +tlrc box size.
15 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to afni.c, afni_func.c, afni_slice.c, afni_warp.c, etc., to allo
w
MRI_rgb-valued datasets. These can be created in to3d from ppm input
files.
11 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program 3dAFNItoMINC.c, and new function thd_mincwrite.c.
* Fixed bug in thd_mincread.c: it formerly scaled float inputs, which
apparently is wrong.
10 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Remove malloc.h include from mpeg_encode files for OS X compatibility.
* Modify thd_automask.c to only keep largest connected component.
* New program 3dAutomask.
* Modified a few programs to use -automask as a synonym for -autoclip
3dAutoTcorrelate.c, 3dTcorrelate.c, 3dToutcount.c, and 3dTqual.c.
09 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Some minor changes to machdep.[ch] to make AFNI work on Mac OS X 10.1.3.
05 Apr 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added (x,y,z) coord printout to 'Where Am I' window.
* Modified imseq.[ch] to remove ALLOW_ZOOM conditional, and allow zoom/pan
from 'z', 'Z', and 'p' keystrokes.
29 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.c to accept multi-plot timeseries.
* Added plug_nth_dataset.c to generate multi-plot timeseries.
* Fixed bug in to3d.c that disabled -4swap option (from 07,MAR,2002).
28 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added function mri_move_guts() to mri_free.c, in preparation for multi-
plotting in afni_graph.c.
27 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dinfo.c, thd_info.c to have a -short option.
* Modified imseq.c to have isqDR_options save the output filter, rather th
an
reset it. (Otherwise, Left-is-Left loses the new default 'Save to .ppm'
.)
* Modified parser.f and 3dcalc.c to include a mad() function.
26 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to save zoomed images in filtered Save many code as wel
l
(including animations). Also set 'Save to .ppm' as the default save mo
de,
if possible.
25 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to crop saved zoomed images if ordered by environment
variable AFNI_CROP_ZOOMSAVE.
23 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to zoom and draw overlays on Save One images.
22 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_dup.c to correctly shift RGB images by 1/2 pixel.
* Modified afni.c to correctly draw coordinates for lines shifted by 1/2 p
ixel.
* Modified afni.c and afni_pplug_env.c to allow user to draw crosshairs wi
th
lines instead of overlay pixels.
18 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to make it necessary to use -niml or AFNI_NIML_START to
have NIML listening activated from the beginning.
17 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_niml.c to disable NIML listening if all potential sockets
are busy. This is to prevent an endless series of error messages
when 2 AFNIs are running at once.
* Modified afni.c to add option '-noniml'.
16 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to not start NIML until the startup timeout is called.
Otherwise, very early data might try to popup a window before that
is possible. Also, made NIML be turned on by default.
* Modified afni_niml.c to have the popup messages include the I/O and
processing time for large data elements.
* Modified imseq.c (and afni_pplug_env.c) to keep panning mode on if
AFNI_KEEP_PANNING is yessish.
* Modified xim.c to speed up rgb_to_XImage(), by doing TrueColor and
PseudoColor in separate functions.
15 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c ISQ_show_zoom() function to discard old zoomed image if
the pixmap had to be re-created.
* Modified mri_dup.c to do 3x RGB upsample in special function, too.
* Modified imseq.c to do panning with Button1 when the new 'pan' button
is on - the 'old' arrowpad buttons have been excised.
14 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_dup.c to use 171/256, 85/256 as approximations to 2/3, 1/3
for
upsampling byte arrays by 3 - this avoids a division, and should be
faster. Also a function to do upsample by 4 of 2D RGB images all at
once - this turns out to be worth the effort - speeds up nearly twice.
* Modified thd_loaddblk.c to check if sub-bricks are all the same datum; i
f
not, always uses malloc() and also prints a warning to stderr.
* Incorporated changes from Doug Ward
* The group statistical analysis programs (3dANOVA, 3dANOVA2, 3dANOVA3,
3dRegAna, 3dMannWhitney, 3dWilcoxon, 3dKruskalWallis, 3dFriedman), wh
en
creating an AFNI 2-subbrick dataset or a bucket-type dataset, previou
sly
used the following format for the output datum types
'intensity' sub-bricks -- same as input dataset
statistical sub-bricks -- scaled short integer
The above programs have been changed so that all output subbricks
will now have the scaled short integer format.
* Modified program 3dbucket, so that if there is more than one input
dataset, it will copy the command line history from the first input
to the output bucket dataset.
13 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to not reload the zoomed Pixmap if the image isn't new.
This speeds up scrolling the zoomed image quite a lot.
* Modified coxplot/plot_x11.c to work properly if the first call to the
rendering function is into a Pixmap instead of a Window.
* Fixed a bug in niml.c that created NIML_TRUSTHOST_%2d environment variab
le
names - should have been NIML_TRUSTHOST_%02d (D'oh).
* Modified mri_dup.c to upsample byte-values images by 2/3/4 in special co
de.
This makes imseq.c zooming faster.
12 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Implemented 'zoom' feature in imseq.c (with a little help from bbox.h).
* Modified mri_dup.c to allow linear as well as heptic upsampling.
Use this for faster zooming in imseq.c.
11 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to have SUMA overlay box and line color environment
strings set to 'none' mean to skip that overlay step. (The lines
look better without the boxes.)
10 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot/plot_cox.c, plot_x11.c, plot_ps2.c to allow circles.
* Modified afni.c, afni_pplug_env.c to use environment variables to set
SUMA overlay box size and color.
* Modified imseq.c so that 'q' keypress causes a window close (to make
this window like the various graph windows).
* Modified afni_niml.c to receive SUMA_ijk triangles.
* Modified afni.c to draw triangle/slice intersection lines.
* Modified afni.c to allow specification of AFNI_FIM_IDEAL on startup.
* Modified afni.c to set Dummy session directory to 1st argv directory.
08 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.c and afni.c to add 2 environment variables to
let user set the initial graph baseline parameters.
* Modified afni_func.c, afni.c, and afni.h to allow the Define Function
value label to be recomputed/redisplayed even if only 1 image
window is open.
08 Mar 2002, RC Reynolds, plug_crender, level 4 (SUPER), type 1 (NEW_PROG)
added rendering plugin to afni
07 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.c (and afni_pplug_env.c) to make Button3 popup
text info window be a scrollable textwin rather than a menu popup
if the number of lines is too long; 'too long' is defined by new
environment variable AFNI_GRAPH_TEXTLIMIT.
* Modified mrilib.h to add field 'was_swapped' to MRI_IMAGE struct.
Then modified mri_read.c to set this field if it auto-swaps the
image on input. Then modified to3d.c to skip doing -2swap/-4swap
on such images.
06 Mar 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Many changes over the last few weeks to include NIML support for
talking to Ziad Saad's SUMA program.
28 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a small problem with thd_info.c (damn you, Jim Haxby).
* Incorporated a few more 3dDeconvolve changes from Doug Ward.
* First cut at putting niml.[ch] into AFNI, along with afni_niml.c.
27 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified various files to replace 'AGNI' with 'SUMA' (SUrface MApper).
For example, we now have afni_suma.[ch] instead of agni.[ch].
26 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to fix up the bucket widgets in AFNI_setup_viewing() aga
in
(cf. 29,JAN,2002)
25 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Adapted modified 3dDeconvolve.c from Doug Ward.
* Modified thd_getpathprogs.c to skip path elements that aren't directorie
s
(some people have no clue, do they?).
19 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dAutoTcorrelate.c to add '-time' option.
07 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to allow AFNI_RESCAN_METHOD environment variable to
choose old rescan method (cf. 28,DEC,2002).
06 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Adapted modified plug_histog.c from Vinai Roopchansingh (added the
'Output' option to write results to a file).
05 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Put #undef USE_TRACING in FD2.c, since it uses STATUS() for something
else.
04 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_getpathprogs.c to correctly skip searching the same
directory twice, rather than the cheap (strstr) way done before.
The old way caused problems when /usr/bin/ was ahead of /bin/,
for example.
* Similar changes to NLfit_model.c, afni_plugin.c, and thd_get1D.c.
* Removed the NULLIFY_ON_DESTROY() call for the whereami textwin in
afni.c, since the kill function for this window does the same
thing. This may be the cause of the bug that Jill Weisberg
reported (that the whereami function stops working and then
crashes AFNI when the user presses the Quit button).
02 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added extreme_proj() to afni_transforms.c.
01 Feb 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Put most transform functions from afni.c and imseq.c into new file
afni_transforms.c.
* Added 3dFDR.c from Doug Ward, and some changes to 3dDeconvolve.
31 Jan 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to allow scrollbars on the Disp button dialog, if
AFNI_DISP_SCROLLBARS is yessish.
* Modified imseq.[ch] and afni.[ch] to provide slice_proj projection
functionality.
30 Jan 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program 3dAutoTcorrelate.c for PAB.
29 Jan 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c function AFNI_setup_viewing() to correct problem when
viewing the same functional bucket in two controllers - the bucket
widgets might not get set up correctly due to false memories.
28 Jan 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified cs_qhull.c to use centroid instead of normal for midpoint.
13 Jan 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified Makefile.solaris28_gcc on hador system - plugins would no longe
r
load. Use of GNU ld instead of UCB ld fixes this, but for unknown
reasons. Evil spirits?
08 Jan 2002, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifications to make AFNI work under CYGWIN (www.cygwin.com)
- Removed shm stuff from thd_iochan.c
- Compile plugins directly into afni.exe (no dlopen)
- Changing Makefile.cygwin and Makefile.INCLUDE to make
PLUGIN_init() function have different names for each
plugin compiled on CYGWIN
- At this time, 3dNLfim, 3dTSgen, plug_nlfit, and plug_wavelets
are not compiled for CYGWIN since they present difficulties.
28 Dec 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified matrix.[ch] and RegAna.c to speed up some of Doug Ward's
matrix-vector calculations, to make 3dDeconvolve faster. Makes
it about 22% faster on an Athlon/Linux box.
21 Dec 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed up some rescan session problems with AFNI_GLOBAL_SESSION datasets.
(We don't want to let them be destroyed or descendant-ized.)
20 Dec 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified ge_header.c to use -verb option to print out more stuff.
* Modified to3d.c to set default dataset type to ANAT_EPI_TYPE (-epan)
if user is creating a 3D+time dataset.
* Modified mri_read.c and to3d.c to correctly calculate and use
MRILIB_xoff and MRILIB_yoff for GEMS images.
* Modified afni.h, afni.c, afni_func.c to implement AFNI_GLOBAL_SESSION
environment variable.
13 Dec 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified bbox.c to do XUngrabPointer if user presses Button-2 to try
to popup a list chooser for optmenus. If the optmenu is inside a
popup menu, Motif never does an XUngrabPointer, thus freezing the
X server until afni is killed from outside. This seems to avoid
that problem.
11 Dec 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed stupid errors in the cursor stuff, and propagated the changes
to more places, so that most AFNI windows should now be properly
cursorized.
* Fixed bug in to3d.c - 1 slice with TR=0 on command line would crash.
* Modified bbox.[ch] to allow user to set menu column length via
environment variable AFNI_MENU_COLSIZE.
* Modified bbox.c to allow user to use Button-3 to popup a list chooser
for optmenus.
07 Dec 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3daxialize.c to allow arbitrary orientation of output
(-orient option). Also changes to ORCODE() macro in thd.h
and to3d.h, and added new function to thd_fdbrick.c.
* Modified imseq.c, afni_widg.c, afni.c, afni_graph.c, plug_render.c
and xutil.h to change cursor slightly when it moves over a
window that has a hidden Button-3 popup menu.
* Modified 3dTstat.c to have NOD (no-detrend) versions of -stdev
and -cvar.
* Modified afni_widg.c to implement AFNI_START_SMALL.
04 Dec 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Cleaned up mri_read.c and to3d.c a little.
* Got some small changes to 3dIntracranial.c from Doug Ward (-nosmooth).
* New program ge_header.c prints out GEMS header information.
03 Dec 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to mri_read() in mri_read.c to understand GEMS headers.
* Changes to to3d.c to understand the GEMS header stuff, including
a default TR (if user supplies TR=0).
29 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* mri_write_analyze() function to write an MRI_IMAGE to Analyze files.
* 3dAFNItoANALYZE program to write a dataset to Analyze files.
* Added -prefix option to 3dclust.c.
28 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read.c to also allow floatizing of Analyze .img files,
and guessing at orientation via SPM.
27 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read.c to apply the 'funused1' entry in the Analyze .hdr
file as a scale factor.
* Added mri_scale_inplace() function (mri_scale.c).
21 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_iochan.[ch] to set an error string in some functions.
This can be retrieved with iochan_error_string().
* Modified afni_plugout.[ch] to listen for connections on socket ports
7955..7959.
* Modified afni_plugout.[ch] to break input command strings from plugouts
into substrings (separated by NULs) and execute them all. This will
let AFNI catch up when a plugout races ahead during a dataset read
or a window resize, for example.
20 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot/plot_cox.c to have functions to convert between
user and memplot coordinates.
* Modified afni_driver.c to remove debug print statements, and to
add some comments.
16 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot/plot_strip.c to add an X at the end of each
evolving graph.
* Modified afni_driver.c to have command SET_GRAPH_GEOM.
15 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added plot_strip.c to coxplot/, for doing timeseries plots with
recyling back to the left when the graph is full.
* Added OPEN_GRAPH_1D (etc.) to afni_driver.c.
* Added cutoff() to afni_plugout.c when it closes a socket.
14 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added OPEN_GRAPH_XY (etc.) to afni_driver.c, to display graphs
from plugout data.
13 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_driver.c to allow OPEN_WINDOW to open a plugin.
* Modified afni_splash.c so that layout code doesn't check plugin
widgets if this is a custom plugin (which won't put widgets
into the 'plint' struct).
12 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imreg.c to have -cmass option for pre-alignment of
center of mass.
09 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Replaced isblank() in afni_driver.c with isspace() - the former
is a GNU extension, the latter is standard.
08 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_driver.c to allow the OPEN_WINDOW function to have
layout parameters geom=, ifrac=, mont=, matrix=, and pinnum=.
07 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_plugout.c to call AFNI_driver() function in response
to 'DRIVE_AFNI' commands.
* Added afni_driver.c and AFNI_driver() function to carry out some
user interface functionality from a plugout
- open windows, close windows
- switch sessions, datasets
- rescan this
- quit
* Added a button to the Datamode->Misc menu to start plugouts.
05 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_dsetto1D.c to break THD_extract_series() into two
functions. The new function THD_extract_array() returns data
in an array supplied by the caller. This is used in thd_median.c
and thd_outlier_count.c to avoid the malloc/free cycle on
thousands of voxel time series.
* Modified thd_cliplevel.c to check bounds on hist[] array when
loading it with shorts, and to increase size of hist[] by 1.
(This last problem was causing to3d to crash.) Also modified
3dClipLevel.c in the same way.
* Modified coxplot/plot_motif.c to disable 'PS->printer' button if
environment variable AFNI_PSPRINT isn't set.
* Modified machdep.c to do enable_mcw_malloc() if environment variable
AFNI_FORCE_MCW_MALLOC is yessish. Modified mcw_malloc.c to have
enable_mcw_malloc() return immediately if it is already enabled.
* Modified qmedmad_float() in cs_qmed.c to free workspace array when
done with it (oopsie).
02 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dmerge.c to protest if an input dataset (for merge)
can't be loaded. Also changed edt_onedset.c to use DSET_LOADED()
macro.
01 Nov 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_mincread.c to allow :step attribute of dimensions
to be missing (default=1), and even to allow the dimension
variables to be missing.
* Modified mri_new.c to use calloc() instead of malloc().
* Modified MCW_choose_string() in bbox.c to use length of 1st line
of label arg as size of text box, rather than strlen(label).
* Modified afni_func.c to change way the 'Read Web' button presents
its chooser, and put some sample Web datasets on the server.
30 Oct 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified MINC stuff to use AFNI_MINC_FLOATIZE environment to
control conversion to internal floats, and to use
AFNI_MINC_DATASETS to control whether AFNI itself looks
at .mnc files.
* Added program 3dMINCtoAFNI.c to re-write a MINC file into an AFNI
dataset; 3drefit may be useful afterwards.
29 Oct 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added thd_mincread.c to read MINC format files as AFNI datasets.
Also changed 3ddata.h, afni.c, thd_initsess.c, thd_mastery.c,
thd_opendset.c, etc., and include subdirectory netcdf-3.5.0/
that hold the NetCDF library.
26 Oct 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added THD_surefit_to_dicomm() to agni.[ch] (from Vecwarp.c).
* Modified agni.c to allow SureFit coord files to be read directly
using in .SURF file.
25 Oct 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added '-q' (quiet) option to afni.c (also affected afni.h, afni_widg.c,
and afni_plugin.c).
* Fixed bug in AFNI_set_viewpoint() in afni.c, so that the AGNI node
is looked up only if we are in 'view brick' mode.
* Added program Vecwarp.c, at the request of David van Essen of Wash U.
22 Oct 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in 3dvolreg.c about -twopass weight brick (noted by
William Gandler of the NIH).
19 Oct 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in imseq.c: if pnmtops was NOT found but epstopdf WAS found,
then the program would crash (this is the Ben Xu memorial bug).
* Modified thd_winsor.c and 3dWinsor.c to have new '-clip' option.
18 Oct 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_loaddblk.c to make THD_load_datablock() have only 1 argumen
t;
the 'freeup' argument is moved to a file-scope variable, and is set
by calling new function THD_set_freeup().
* Modified lots of programs to use modified THD_load_datablock() correctly
.
* Modified DSET_load() macro in 3ddata.h.
* Modified afni.c to use THD_set_freeup() with AFNI_purge_unused_dsets().
* Added macro mri_zero_image() to mrilib.h.
* Modified thd_fdto1D.c to zero output, then only access non-NULL bricks;
this is to prevent crashes when a user tries to graph a dataset that
didn't load correctly (cf. Sally Durgerian).
* On some Solaris systems, displayed to SGI systems (cf. Mike Beauchamp),
Button 3 doesn't always seem to get passed through. The following
changes are to let Button 1 also popup 'hidden' menus
- imseq.c for wbar menu
- imseq.c for wimage menu (if Ctrl or Shift also pressed)
- afni_setup.c for Inten menu
- afni_func.c for Hidden menu (in logo square)
- plug_render.c for Inten menu and Xhair menu (latter is Button 2)
However, these changes don't seem to work - the mouse events aren't
received. Ugh.
16 Oct 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Took new FD2.c from Andrzej Jesmanowicz, with changes to run with X11
TrueColor visual.
01 Oct 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_plugin.c to make plugin alphabetization the default (that
is, the user has to 'setenv AFNI_PLUGINS_ALPHABETIZE NO' to get the
old behavior).
27 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_md5.c to add UNIQ_idcode() function, which produces strings
like 'USA_mFs+P-tnCc1vQQM0UuL0Hg', using a modified Base64 encoding of
the MD5 sum of some system info and the current time.
* Modified thd_base64.c to avoid use of mrilib.h (so it can be easily used
by non-AFNI programmers).
* Modified thd_idcode.c to use UNIQ_idcode() instead of older method.
* Modified 3ddata.h to extend length of MCW_idcode string to 32 (so can
use results of UNIQ_idcode()).
25 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_drawdset.c to have a new drawing mode, 'Filled Curve'.
* Modified mri_read.c to allow .HDR and .IMA suffixes for Analyze
and Siemens files, respectively (in addition to .hdr and .ima).
* Modified mri_read_siemens() in mri_read.c so that if the environment
variable AFNI_SIEMENS_INTERLEAVE is set to 'Y' or 'y', then the
multi-images in a Siemens file are assumed to be interleaved rather
than presented in order.
* Modified to3d.c to have new option -sinter: sets AFNI_SIEMENS_INTERLEAVE
to 'Yes'.
* Modified plug_drawdset.c to do EVERYTHING_SHUTDOWN after Quit is pressed
.
For some reason, this was blocking proper Undo-ing if the user did Quit
,
then restarted the editor.
24 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program 3dcopy.c does what it sounds like: copies datasets.
* Modified plug_drawdset.c to allow the user to make a copy of a
dataset on input, and to have a SaveAs button.
23 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added a setback environment variable to let image label placement be
adjusted.
* Modified afni_widg.c to load a color pixmap for use with the 'wait'
picture, if the visual is TrueColor.
21 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.[ch] to adjust the way labels are drawn.
* Fixed ISQ_saver_CB() bug in imseq.c: when Save:one was active and images
were sent to an output filter, they needed to be forced into RGB mode
even if they were grayscale.
* Changes to afni.c and imseq.c to allow label and agni overlay colors to
be
controlled by environment variables.
* Added function DC_parse_color() to display.[ch] to parse a color string
into
a (float) RGB triple.
20 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to do the overlay plot montage more efficiently
(using less memory).
* Modified imseq.c to draw labels returned by the get_image() function
for each slice, both in single and montage images.
* Modified afni.c to return a label for each slice.
* Modified coxplot/plot_cox.c to have new function, create_memplot_surely(
).
Modified a number of functions/programs to use this instead of looping
over create_memplot() a number of times.
19 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* In imseq.c, realized that the 'Empty Image' memplot was being re-created
multiple times, and this is stupid. Now it is only created once, and
is re-used from then on.
* Also in imseq.c, realized that if last image in a Save sequence is
NULL, and we are saving to an animation, then the animation won't be
written and the saved images will never be deleted. At least they
will be deleted now (animation still won't be written, but at least
an error message will be output).
* Also in imseq.c, added montage overlay plots to function
ISQ_make_montage().
18 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added mri_drawing.c to draw things into RGB images, and mri_coxplot.c,
to use that to draw coxplot stuff into RGB images.
17 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read.c to add new function mri_read_ppm_header(),
and to make mri_read_ppm() scale a PPM image to maxval=255.
* Modified afni_splash.c to look for .afnisplash*.ppm files for the
splash image override.
13 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_plugin.c and NLfit_model.c to properly load .so objects
on Mac OS X (DARWIN).
12 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Wrote thd_autonudge.c and 3dAnatNudge.c to try to fit EPI volume
on top of scalped SPGR volume.
11 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_render.[ch] and plug_render.c to allow depth cueing of
ShowThru overlays (new option ST+Dcue on overlay opacity menu).
07 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified agni.[ch] to put a mask into the vmap to mark the level
of expansion at which the voxel was mapped.
* Modified agni.c to using ENTRY/RETURN.
* Modified agni.c to check for duplicate node id's when creating a surface
.
* Modified afni.c and afni_plugout.c to strip off the vmap mask when
querying this array.
* Modified machdep.c to get the _Xsetlocale() fixup function; added
machdep() to a lot of programs (for Mac OS X compilation).
06 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_plugout.[ch] to have 'NO_ACK' option, so that plugout
messages aren't acknowledged. This is necessary to avoid race
conditions with a plugout that both sends and receives messages.
* Modified afni_plugout.[ch] to allow sending and receiving of SURFID
for surface node identifiers.
* Wrote plugout_surf.c as a demo of the SURFID interchange.
05 Sep 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified machdep.[ch] to provide some support for Mac OSX (Darwin).
* Modified agni.c to do volume map (vmap) correctly, and faster.
30 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot/plot_cox.c to have a flip_memplot() function, for use
in imseq.c graphing overlay.
* Modified coxplot/plot_x11.c to draw a Point rather than a Rectangle
if the rectangle has width=height=0.
* Modified afni.c to draw surface nodes in correct places, rather than
in center of their voxels. Also involved changes to thd_coords.c,
to have new functions for floating point coords in FD_bricks.
29 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Created cs_sort_template.h, a file to generate quicksort functions from
a macro-defined type and macro-defined order.
* Adapted 1st version of agni.[ch] to fit into afni, for surface display.
Changes also to afni.c (to draw the damn thing), imseq.c, and some
other minor junk.
28 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_correlate.c Pearson routine to initialize sums (oops).
26 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified to3d.c to have -save_outliers option.
24 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dTcorrelate.c to have '-polort -1' option.
* Modified afni_friends.c.
* Modified to3d.c, which tried to popup outlier message in batch mode.
Also, made it check for negatives again after 2swap; skip outlier
check if too many negatives (more than 1%); print percentage of
negatives in negatives report.
23 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 3dTcorrelate.c to compute correlation coefficient of
2 3D+time datasets, voxel by voxel.
* New file thd_correlate.c computes various correlation coefficients
between vectors.
* Added constant detrending to thd_detrend.c.
22 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_drawdset.c to allow loading of overlay data from the
TTatlas+tlrc dataset, on a region-by-region basis.
20 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Incorporated revised TD database from San Antone. Also penciled in
the Nucleus Accumbens, since they seem to have missed it.
16 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to hintize the pbar in function AFNI_underlay_CB().
* Modified the outlier stuff in to3d.c some.
15 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dToutcount.c to have a -range option, a la 3dTqual.c.
* Added function THD_outlier_count() to do more or less what 3dToutcount.c
does.
* Used this in to3d.c to automatically check new 3D+time datasets for outl
iers.
14 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified a bunch of programs to use AFNI_logger().
13 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -dt option to 3dcalc.c.
* Added routine AFNI_logger() in afni_logger.c.
12 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in 3dClipLevel.c that used 1 past the end of the histogram
array (bad Bob, bad).
* Added functions thd_median_brick() and thd_cliplevel() in files
THD_median.c and THD_cliplevel.c to the library.
* Modified 3dTqual.c to use these library functions.
* Modified 3dToutcount.c to have -autoclip option.
11 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_scatplot.c to print correlation coefficient.
10 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added TENT() function to parser.f and parser.inc.
* Added thd_dsetto3D.c, to extract/scale a float copy of a sub-brick.
* New program 3dTqual.c computes a 'quality index' of each sub-brick
in a 3D+time dataset.
* Modified 1dplot.c so that -stdin option can read more than 1 column.
09 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 3dZcat.c to put datasets together in the slice
direction.
* (Re)modified to3d.c to allow creation of 1 slice datasets. Hope it
works out this time.
08 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.c and xutil.c to use new environment variable
AFNI_DONT_MOVE_MENUS - if this is 'Yes', then the menu movement
functions will be skipped. Also added this to afni_pplug_env.c.
(As usual, this is in response to a problem on Solaris.)
* Added program 3dZcutup.c to cut slices out of a dataset.
* Modified various functions to work with single-slice datasets.
Probably missing some still.
07 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.[ch] and afni.c to extend graph baseline concept
to have a global baseline for all graphs (that doesn't change when
the user moves around).
* Modified afni_graph.[ch] to add a new Double Plot mode Plus/Minus to
make the transformed function be added/subtracted from the dataset's
time series, so we can see error bars from 3dDeconvolve's
-iresp/-sresp outputs!
* Added afni_pplug_1dfunc.c to make 1DChain pseudoplugin (also affected
afni_func.c and afni_widg.c).
06 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot/plot_motif.c to have plotting window close when
user presses 'Q' or 'q' keystroke in the drawing area.
02 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in waver.c -EXPR option, so that if waveform_EXPR(t) is
called with t < 0, it returns 0.
* Included mpeg_encode directory into AFNI distribution, and added to
Makefile.INCLUDE to make mpeg_encode.
However, neither of these program is made by default.
* Added Sav:mpeg to imseq.[ch].
01 Aug 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Realized that the TT atlas overlay was setup for the small Talairach
box, and most people now have large Talairach box datasets. To make
the system work, modified thd_ttatlas_query.c to allow programs to
load an atlas with 141 I-S slices (the one on disk), or an atlas
with 151 I-S slices (created via zero-padding). Then modified places
that retrieved the atlas dataset: afni_func.c, plug_render.c. Ugh.
* Also modified afni.c so that the 'Atlas Colors' popup button is only
enabled in +tlrc view.
* Modified waver.c to add to -EXPR option.
* Added -stdin option to 1dplot.c.
31 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified xutil.[ch] to add a routine to NULL out an arbitrary pointer
when a widget is destroyed.
* Used the above in afni.c to NULL out the pointer to the 'Where Am I?'
text window when the text window is destroyed because the user
destroyed its parent imseq.
30 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed color pbar hintize alterations when user changes sub-bricks,
in plug_render.c.
29 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.[ch] to add a range hint to the intensity bar.
27 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.[ch] to add 'Sav:aGif' to save a sequence of images
into animated GIF format (using gifsicle or whirlgif).
* Included gifsicle directory into AFNI distribution, and added to
Makefile.INCLUDE to make gifsicle (whirlgif was already there).
However, neither of these program is made by default.
26 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.[ch] to allow 'Save One' to be independent of the
output filter (e.g., so can save a montage into a JPEG file).
25 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_render.c to histogram new dataset bricks and choose
99.5% point as the default upper level for scaling.
* Modified afni.c, afni_func.c, afni_widg.c, afni_warp.c to enable
rendering of TT Atlas regions as overlays in 2D image viewers.
24 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_ttatlas_query.c to return up to 9 results, and to print
a cautionary tail.
* Modified plug_render.c to display TT atlas regions.
13 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* OK, made afni_ttren.c work with the volume renderer.
* Modified mcw_glob.c to only print warning message if allowed to.
Modifed various codes that use MCW_file_expand() to turn such
messages on or off, depending on what I feel like.
12 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added afni_ttren.c, to control the colors of the display of the
Talairach atlas regions (when I get around to it, that is).
11 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified xutil.[ch] to add function MCW_unregister_hint().
* Modified afni.c to add hint/help to 'Where Am I?' textwin (and to
remove help when the window is destroyed).
10 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Where Am I?' Talairach Daemon feature to afni_widg.c, afni.[ch].
Actual calculations done in thd_ttatlas_query.c.
* Modified xutil.[ch] to add function to alter contents of a textwin.
* Added edt_sortmask.c to sort a MCW_cluster based on its contents.
09 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified AFNI_transform_vector() in afni.c to use anat_parent
transformations if the datasets aren't directly related.
* Used this to modify the 'Talairach to' feature (AFNI_talto_CB() in afni.
c)
to allow jumping even if the dataset is not in Talairach view, but just
has a way of transforming the vector to Talairach view.
06 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dUndump.c to print a message if a voxel is written to
more than once.
* Added Doug Ward's changes to 3dDeconvolve.c, 3dConvolve.c, etc.
05 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.[ch] to include CM's from Talairach Daemon database,
and re-enabled the long-dormant 'Talairach to' button.
* Added option '-nosum' to 3dclust.c.
* Modified thd_loaddblk.c to skip byte order tests if all sub-bricks
have byte datum.
03 Jul 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to correct usage of pnmtotiff, which is NOT the
same as ppm2tiff (first one writes to stdout, second to a file
named on the command line).
29 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program strblast.c to blast strings out of image files.
* Modified 3dclust.c to use THD_open_dataset() instead of
THD_open_one_dataset().
27 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added ability to save images in various formats (.jpg, .gif, etc.)
to imseq.[ch], using external programs such as ppmtogif, etc.
26 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added function THD_is_executable() in thd_filestuff.c.
* Added thd_getpathprogs.c to get list of all executables in the path.
22 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a bug in 3dUndump.c where it checked the wrong value against
the z coordinate bounds - it would report illegal inputs when
the (x,y,z) values were in fact legal.
19 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3drotate.c to take the new -dfile/1Dfile options, per
the request of David Glahn of UCLA.
18 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read_ascii() in mri_read.c to skip lines that start
with '#' character.
07 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add cs_qhull.c to drive qhull program and compute Voronoi areas
on sphere surface.
06 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added directory qhulldir/ to contain the qhull program from UMN.
* Fixed afni_vcheck.c to reflect the new webserver.
05 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_plugin.c to move some routines into the 'always
compiled' section; and afni_plugin.h to reflect this change.
Small changes also to afni.h, afni_func.c, and afni_pplug_*.c.
(All of this is to get afni to compile again without plugins.)
04 Jun 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_iochan.c iochan_fork_delay() to retry communications,
and to print more error messages.
* Added DONT_USE_DEBUGTHISFILE to machdep.h and debugtrace.h.
24 May 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_plugin.c to fprintf(stderr) the error message if
a plugin library cannot be loaded into the system. (This way
it always appears, even if trace is turned off.)
23 May 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_iochan.[ch] to add function iochan_fork_delay(),
which allows relays of data from a shm IOCHAN to a tcp IOCHAN
through a child process.
22 May 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_iochan.[ch] to add function iochan_recvloop(), which
loops to receive as much data as possible without waiting.
18 May 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_plugin.[ch] to STATUS() an error message if a
plugin library cannot be loaded into the system.
16 May 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified waver.c to add new -tstim option (for specifying stimulus
times directly on command line).
10 May 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a bug in to3d.c with the Analyze/Siemens header geometry info
it was only processed AFTER the autosave test was executed. It was
moved before the autosave. Also added the -zorigin option to let
the user set the slice offset (a la 3drefit).
09 May 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a scale-resize bug in Solaris (why does this keep happening,
and only on Solaris?!) in afni.c, afni_func.c, and plug_render.c.
04 May 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_loaddblk.c to print a message if a mmap()-ed file isn't
big enough for the dataset byte count.
30 Apr 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mcw_glob.c to print an message if an attempted expansion
produces no files.
25 Apr 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c recording a little.
* Fixed a bug in 3dAttribute.c in which the tross_Expand_string()
result might be NULL, in which case printing it would crash
on some systems. Also, free()-ed the data from that call.
24 Apr 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'record' capability to imseq.[ch].
23 Apr 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.c to draw 'EMTPY IMAGE' string into image window if
a NULL image is returned.
20 Apr 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'addto_args' to a bunch of programs, to let them use the '-@'
command line switch.
* Added call to machdep() in a bunch of programs.
18 Apr 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added some more printouts to 3dcalc.c and thd_loaddblk.c when malloc()
fails on dataset input.
* Added '-sum' and '-sqr' options to 3dMean.c.
* Added program 1dsum.c.
* Added machdep.c to do machine-dependent runtime startup (supplementing
machine-dependent compiletime stuff in machdep.h).
10 Apr 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a bug in 3dvolreg.c, where the '-base dset' option used a
sub-brick index 'bb' that was no longer initialized (bug reported
by Tom Ross of MCW).
03 Apr 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified xim.[ch] to add a 'force rgb' option to function XImage_to_mri(
),
so that one can always be sure of getting a MRI_rgb image (and so be
sure of writing a PPM file with mri_write_pnm()). Modified imseq.c and
afni_graph.c to fit the new usage.
30 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Rota' buttons to afni_widg.c and plug_render.c, to rotate
the colors on the pbars.
* Added range hints to the pbar in afni_func.c and plug_render.c.
26 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c, afni_widg.c to add a 'Read Web' button.
* Modified thd_fetchdset.c to allow fetch of *.1D files as well.
23 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added thd_fetchdset.c, to get a dataset from a Web link. This is
called from THD_open_dataset() in thd_mastery.c. Thus, you can
now do something like
afni -dset http://some.place/dir/anat+orig
and see the dataset!
22 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -save option to 3dToutcount.c, to leave markers of outliers
behind.
* Added script moveAFNI to install changed files from afni98.tgz into
the current directory.
21 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot to draw filled rectangles when thickness is set
to -1.0. Files affected are coxplot.h, plot_cox.c, plot_ps.c,
plot_ps2.c, and plot_x11.c.
* Added program 1dgrayplot.c to plot timeseries files (vertically)
in grayscale, a la SPM.
* Modified afni_plugin.c to remove the MCW_TIMER_KILL from the
ButtonPress frivolity in image popups. Also, hid this stuff
behind the NO_FRIVOLITIES macro and NO_frivolities global variable.
* Added program 3dToutcount.c to count outliers at each time point in
a 3D+time dataset (idea from Bill Eddy).
20 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 3dDeconvolve.c update from Doug Ward.
* Modified plug_histog.c to add 'Aboot' feature.
19 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in thd_dsetrow.c, where putting a row back in for byte
or float cases didn't have break statements, so it would be
put twice, which is real bad (i.e., segment fault).
* Added Linear Fillin to plug_drawdset.c.
15 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in thd_shift2.c: when the shift was larger than the data
line size, buffer overrun could occur. In this case, the proper
result is all zeros, so that's what I substituted.
12 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read.c to read Siemens Vision format .ima files.
* Modified mrilib.h to have global variables MRILIB_* that hold
orientation info from image files, if present. Modified to3d.c
to use this information.
* New program siemens_vision.c prints out info from the .ima format
files' header.
09 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed 1deval.c so that '-v' option becomes '-verb' (since '-v' had
another meaning in that program). Also modified several other
programs so that '-verb' is accepted (instead of '-v' or '-verbose').
* Modified imseq.c to de/re-sensitize overlay opacity arrowval when
'See Overlay' is turned off/on.
08 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added median+MAD function to cs_qmed.c.
* Added display of median+MAD to popup stats in afni_graph.[ch].
* Added thd_dsetrow.c, thd_rowfillin.c, 3dRowFillin.c to do row filling
between gaps (zeros) of like values. Intended to complement the
drawing plugin.
* Modified plug_render.c to allow user to display the xhairs in the
color overlay (meaning they can ShowThru).
07 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified imseq.[ch] to add controls and functions for translucent color
overlays, if X11 Visual is TrueColor.
* Modified to3d.c, afni_plugin.c, and plug_render.c to turn off the
overlay opacity arrowval for their particular image windows
(since they don't use overlays anyhoo).
* Modified rwc.xbm logo bitmap to include NIH logo along with MCW logo.
06 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified display.[ch] to store RGB bytes for the underlay and overlay
colors in the MCW_DC structure. This is preparation for allowing
direct RGB overlays into imseq.c.
* Modified mri_new.c (and mcw_glob.c) to allow use of the special filename
ALLZERO in 3D: input. This will make it simple to create an empty
dataset using to3d, for example.
* Added -min and -max options to 3dTstat.c.
* Modified 3dClipLevel.c to use all sub-bricks instead of just the first.
* Added function ISQ_overlay() into imseq.[ch], to do the overlaying of
underlay and color of MRI_short and MRI_rgb in all cases.
05 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified Ziad Saad's plug_delay_V2.h to use remainder() instead of
drem() for Solaris, since Solaris doesn't have that BSD function
for some stupid SysV reason.
04 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program ent16.c computes 16-bit entropy of stdin stream. Can be
used in a script to decide when to gzip datasets.
03 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dTsmooth (yet again) to allow for different options for
dealing with points past the beginning and end of time.
02 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added thd_entropy16.c to compute entropy (bits/short) of a dataset.
* Used entropy to force gzip of highly redundant datasets in
thd_writedblk.c -- if AFNI_AUTOGZIP is on.
* Modified afni_environ.c so that yesenv() and noenv() use my_getenv().
* Modified afni_pplug_env.c to include AFNI_AUTOGZIP.
* Modified afni.c to put DBG_trace= statements inside #ifdef USE_TRACING.
* Modified 3dZeropad.c to not overwrite existing datasets [Oopsie squared]
.
* Modified 3dmerge.c to print warning message for default indexes
(if -1dindex and/or -1tindex is not used).
* Added 3ddelay.c from Ziad Saad.
01 Mar 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Max Count' input to plug_histog.c.
* Fixed incorrect error message for '-nrep' option in 3dWinsor.c.
* Added -blackman and -hamming options to 3dTsmooth.c [per MSB].
29 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_initdkptr.c to properly treat directory components stored
in prefixname. [Ugh]
28 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program 3dZregrid.c is for resampling a dataset along the slice-
direction to change the grid spacing, etc. Mostly intended to
fixup user stupidities (e.g., not acquiring data on the same subject
using the same slice thickness; d'oh!).
* Modified thd_filestuff.c to remove '/' from THD_filename_ok() function.
This lets the '-prefix' option of 3d* programs put the output dataset
into a new directory. New function THD_filename_pure() also checks
for the '/'.
27 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added macro SAVEUNDERIZE() to xutil.h, and used it to make popup
menus have the SaveUnder property in imseq.c, afni_graph.c,
afni_widg.c, and plug_render.c.
* Modified imseq.c to use AFNI_IMAGE_MINFRAC environment variable
to set minimum size for image windows. Also added this to the
variables that can be controlled by afni_pplug_env.c.
* Added fields does_saveunders and does_backingstore to display.[hc]
(but don't use them anywhere - yet).
* Modified thd_mismatch.c to do MISMATCH_DELTA only if voxel sizes
differ by at least a factor of 0.001 (rather than perfect ==).
Also fixed a typobug where the datasets would always compare
as identical.
* Modified 3dvolreg.c to fail if stupid users try to register dataset
to base that doesn't match.
26 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plot_cox.c to allow copying, rescaling, and appending of
vector plots, and plot_x11.c to allow setting rendering to a
sub-box of the window (rather than the whole window).
* Modified imseq.[ch] to allow fetching of a vector plot to be
rendered into the window.
* Modified afni_splash.c to draw 'friends' stuff into the splash
screen (after the first popup).
* Added function mri_zeropad_2D() in mri_zeropad.c. Changed name
of MRI_zeropad() to mri_zeropad_3D() in edt_volpad.c.
22 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 3dClipLevel.c to estimate the cutoff value to excise
background regions from anatomical datasets (especially EPI).
* Added AFNI_CWD variable to afni_pplug_env.c, to let user change
working directory (where output files like 'Save:One' go).
* Modified 3dOverlap.c to optionally save counts to a new dataset.
* Fixed thd_mastery.c so that works properly (<= vs. <).
21 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to disable use of mmap() from malloc() on Linux
(malloc() would fail when memory was still available!).
* Modified thd_mastery.c to force dset[] inputs to be relabeled
as bucket types if they are not time-dependent. This is to
prevent interpretation as fico, etc.
* Modified 3dmerge.c to allow use of sub-brick selectors on input
datasets.
* Modified thd_trusthost.c to make it easier to add hosts by name
or by number, using a new function TRUST_addhost().
* Added function PLUTO_turnoff_options() to afni_plugin.c; used this
in plug_realtime.c to turn off all input options after processing.
* Added AFNI_TRUSTHOST to afni_pplug_env.c so that user can add trusted
hosts (for plugins/plugouts) interactively.
* Modified thd_mastery.c and thd_loaddblk.c to allow for sub-ranging
on dataset input, using the syntax on the command line.
20 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added EXIT and TRACEBACK macros to debugtrace.h.
16 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added traceback information to mcw_malloc.c.
* Added program 3dOverlap.c.
* Added function THD_newprefix() in thd_newprefix.c.
15 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added thd_tshift.c, which does what 3dTshift.c does (in place).
* Used this to add -tshift option to 3dvolreg.c.
* Also added -ignore option to 3dTshift.c.
14 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dvolreg.c to include -rotparent/-gridparent options, a la
3drotate.c.
* Edited edt_volpad.c to include new function MRI_zeropad().
* Modified thd_read_vecmat.c to include '-rotate ...' input option.
* Added new function THD_rota3D_matvec() to thd_rot3d.c.
* Added multiply and inverse macros for double vecmats to vecmat.h
* Moved function DBLE_mat_to_dicomm() from 3drotate.c to thd_rotangles.c.
* Replaced all copies of axcode() and handedness() with the library
calls to THD_axcode() and THD_handedness() in thd_rotangles.c
(changes to 3drotate.c, 3dvolreg.c, plug_nudge.c, plug_realtime.c,
and plug_volreg.c).
13 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_shear3d.c function rot_to_shear_matvec() to modify the
input matrix to make sure it is orthogonal (using the transpose of
DMAT_svdrot(q) as the orthogonal matrix closest to q). User-input
matrices may not be precisely orthogonal, which leads to problems
in the shear calculation. Ugh. Squared.
* Added function THD_rotcom_to_matvec() to thd_rotangles.c -- this compute
s
the matrix/vector of a transformation, given the '-rotate .. -ashift ..
'
string.
* Modified thd_zeropad.c (and 3dZeropad.c) so that padding can be specifie
d
in mm instead of slices.
12 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified edt_volpad.c to allow for unsymmetric padding.
* Modified thd_zeropad.c to allow for producing an empty copy of the
zero-padded dataset (so that you have to fill it up later).
* Modified 3drotate.c and 3dvolreg.c to adjust the time-offset z-origin
when the new dataset axes z-origin is adjusted.
* Added a rint() function to mri_free.c (why there? why not?) if NO_RINT
is defined in machdep.h -- that way I don't have to worry about it.
* Modified 3drotate.c to shift time-offsets when the dz is large enough
to warrant it.
* Modified 3drefit.c to add new '-notoff' option, to reset time-offsets
to zero.
* Modified to3d.c to include 'AFNI' in fallback resources, per the
suggestion of J Bacon of MCW (copying what AFNI itself does).
08 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Debugged several stupid errors in 3drotate.c changes of yesterday.
* Implemented program cat_matvec.c to catenate matrix+vector
transformations.
* File thd_read_matvec.c reads a matrix+vector (THD_dvecmat; cf.
vecmat.h) from a file, or from a dataset attribute.
07 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dZeropad.c to have '-z' option to add slices (evenly) in
the dataset z-axis (slice) direction.
* Modified 3drotate.c to deal with -rotparent and -gridparent options.
06 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified vecmat.h to have separate types and macros for float and
double vectors/matrices. Modified all places that used the old
'FLOAT_TYPE double' method to use the new types/macros (mostly
the 3D rotation codes).
* Modified 3dvolreg.c to write rotation parameters, matrices, etc.
to the header of the output dataset.
05 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added mayo_analyze.h to define the structure of an ANALYZE 7.5 .hdr
file, and then added mri_read_analyze75() to mri_read.c.
* Modified to3d.c to use image dimensions if they are set from the
image file (as is possible with ANALYZE .hdr files, for example).
* Modified mri_new.c to set dw=-666 as a flag that the d? variables
defaults of 1.0 haven't been changed.
* Modified thd_rot3d.c to allow setting of zeropad amount via
environment variable AFNI_ROTA_ZPAD.
* Modified 3drotate.c and 3dvolreg.c to use new command line option
'-zpad n'.
* Modified to3d.c to use -zpad option to add zero slices in the z-directio
n.
Also added attribute to header (TO3D_ZPAD) to mark this fact. When suc
h
a dataset is used with -geomparent, then it's zero padding will be
subtracted off when setting the new dataset's origin.
* Modified 3dAttribute.c to have '-all' and '-name' options.
02 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added function NIH_volpad (edt_volpad.c) to do zeropadding on 3D arrays
- adapted from thd_zeropad.c.
* Added THD_rota_setpad to thd_rot3d.c to set zeropadding amount for
rotations.
01 Feb 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_info.c to print dataset center (in addition to box edges).
* Added thd_center.c (dataset center vector) and thd_mismatch.c (check if
2 datasets are matched for voxel-wise comparisons).
* Added program 3dAttribute.c, for printing out values of attributes from
dataset header files (for use in scripts).
31 Jan 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_zeropad.c to keep the slice-dependent time shifts (toff_sl)
when adding/removing slices in the z-direction.
29 Jan 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added DEBUGTHISFILE macro to debugtrace.h, and used it in thd_shear3d.c.
* Modified 3drotate.c so that input of something like
-ashift 10R 0 0
won't have the 0s clobber the 10R; 0s with no direction code suffix wil
l
now be skipped in the computation of the dataset-coordinate shift.
* Added a few words to README.copyright, and added a Q/A about it to the F
AQ.
* Added new program 3dMean.c.
26 Jan 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Converted dbtrace.h to debugtrace.c and debugtrace.h. This is the
start of an effort to incorporate traceback into all AFNI and
mrilib functions. As part of this, removed THD_DEBUG stuff from
all library functions.
25 Jan 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mcw_malloc.c to use a hash table instead of a linear table.
This speeds things up a lot. Also added a serial number to each
allocation, to help in identifying the order -- the dump is now
sorted by serial number.
* Incorporated Matthew Belmonte's codes plug_threshold.c and
plug_permtest.c into the system.
24 Jan 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dclust.c to use '-dxyz=1' option.
* Modified afni.c so that graphs of anat buckets interact correctly when
the anat bucket chooser is changed, or the graph 'time index' is set.
23 Jan 2001, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c MAIN_workprocess() function to exit properly when
the 'nodown' variable is set. Before, if a layout was set, then
the layout code did the splashdown, and then the MAIN_workprocess()
never signaled that it was done.
* Modified thd_trusthost.c to use '192.168.' as the prefix for Class B
subnets, rather than '192.168.0.'.
* Modified mrilib.h to change my e-mail address macro.
16 Jan 2001, RW Cox, AFNI-general, level 5 (SUPERDUPER), type 0 (GENERAL)
Older History stuff
===========================================================
== All changes from this date onwards were made at the NIH ==
===========================================================
09 Dec 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dNotes.c and thd_notes.c to allow user to replace the History
note, rather than just append to it.
* Modified 3dvolreg.c to make the -twopass feature more robust for
registering SPGR images. Changes included a coarse grid search for
an initial shift, and fading out the weights along the edges.
06 Dec 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_pcor.c routine PCOR_get_perc to zero out the results
if the last reference has no range (previously, it only zeroed
out the coef[] array, not bline[]).
* Added GPL/MCW Copyright notices to many many *.[ch] files.
05 Dec 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Included Vinai Roopchansingh's modified 3dhistog.c; this version
adds the '-mask' option.
* Fixed a bug in the PICTURE_ON/OFF macro (afni.h) so that it is
only meaningful for dataset viewing (not for the -im case).
01 Dec 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Included Vinai Roopchansingh's modified plug_copy.c; this version
allows the user to change the datum type, when doing a zero fill.
* Added the 'License Info' button to the Datamode->Misc menu.
28 Nov 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified AFNI_plugin_button() in afni_plugin.c to allow user to
have plugin buttons sorted alphabetically.
* Fixed bug in plug_nudge.c where the interpolation mode was
set improperly.
27 Nov 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_nudge.c to reload sub-brick statistic after moving it.
24 Nov 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_render.c to eliminate duplicate rendering of datasets
when loading a script that changes dataset index. This was caused
by the dataset index CB routine calling draw, and then the script
controller calling draw again. Now, the routine that loads the
widgets from the rendering state sets a variable that stops drawing
if it should occur, then unsets this variable after widgets are
loaded.
* Modified 3drotate.c to have new -points option, to rotate a set of
(x,y,z) triples using the same rotation as would be used for a
dataset brick.
* Modified 3dUndump.c to check (x,y,z) coordinates for validity.
20 Nov 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in -rlt+ option of 3dTcat.c: qmid was 0.5*ns, but
should have been 0.5*(ns-1). This makes the baseline wrong
in each voxel.
16 Oct 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified fftest.c to allow use of FFTW; do 'make fftwest' and
run with nvec = -1.
13 Oct 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_realtime.c to insert its own Xt event loop to deal
with interface-freeze when the images are being slammed in as
fast as possible (function RT_process_xevents).
12 Oct 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.c to redraw with autoscale when matrix or
length is changed by an external (isqDR_) command (not by
the user directly).
* Modified coxplot/plot_motif.c to get initial geometry of graph
shell from an environment variable.
* Minor changes to plug_realtime.c to make various things nicer.
11 Oct 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Replaced XtAppAddWorkProcess in afni.c with PLUTO_register_workproc,
since on Mandrake 7.01, dual P-III, XFree86 4.01 system, the
realtime plugin workprocess doesn't start properly (some
interaction with the startup workprocess, which does not occur
on other systems).
* Modified afni_splash.c to change controller crosshairs to Single
mode if montage spacing is 1.
* Modified afni_graph.c to change grid when program alters pin_num
(but not when user does directly).
* Modifed plug_realtime.c to start work process after a timeout.
* Added PLUTO_register_timeout() afni_plugin.[ch], to execute a
function after a given number of ms.
09 Oct 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Enabled startup of RT plugin, and control of all options, via
environment variables AFNI_REALTIME_Something.
* Modified PLUTO_string_index() in afni_plugin.c to ignore blanks
and case.
04 Oct 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Put most of the work of 3dZeropad.c into function thd_zeropad.c
instead.
* Added plug_zeropad.c.
01 Oct 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Wrote program 3dUndump.c (create a dataset from an ASCII list
of voxels, like an inverse to 3dmaskdump.c).
29 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.[ch] to move FIM and Opt menus onto private
menubars. (Got rid of grapher->option_mbar everywhere.)
* Also put a Form inbetween the afni_graph shell and the drawing
area. The option_rowcol that holds all the menu buttons is
now a child of the Form, not the drawing area. This makes
it possible to popup the menus with Button3 (the Button3
popup on the drawing area interfered with this).
27 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Program xiner.c writes out Xinerama info about the display, if
it is available. This can be used to generate an X11 resource
AFNI.xinerama.
* If AFNI.xinerama is detected, then new routine RWC_xineramize (in
xutil.c) can be used to adjust location of a rectangle to be
sure it fits on a sub-screen. Older routine RWC_visibilize_widget
now uses this. New callback RWC_visibilize_CB can be used to make
sure menus pop up entirely on one sub-screen.
* Many places now use visibilize to make sure dialogs and menus pop
up on 1 sub-screen. See, for example, all uses of the function
RWC_visibilize_widget() and the macro VISIBILIZE_WHEN_MAPPED().
25 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -layout option to allow user to control initial window setup.
Most changes in afni_splash.c, but also in afni.c, afni_widg.c,
afni.h, etc.
* Modified imseq.c to detect Expose events that have resized the
image display window -- this happens sometimes when using -layout.
22 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added isqDR_setifrac and isqDR_setmontage to imseq.c.
* Added graDR_setmatrix, graDR_setgrid, and graDR_setpinnum to afni_graph.
c.
* Added PLUTO_set_topshell() to afni_plugin.c, and made several
PLUGIN_CALL_IMMEDIATELY plugins use this to set the toplevel shell
for later AFNI manipulation.
* Modified afni_graph.[ch] to allow a graph window to be opened for a
dataset of length 1.
* Added textgraph mode to afni_graph.c, and also changed the baseline
pushbutton to a toggle.
21 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 32 to mri_nsize.c.
* Added AFNI_SPLASH_XY to afni_splash.c.
15 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -nscale option to 3dmerge.c
14 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added check of grid spacings to 3dvolreg.c
13 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Finalized -twopass changes to 3dvolreg.c.
* Add -duporigin option to 3drefit.c.
11 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -dxyz=1 option to edt_*.c, to allow clustering and filtering
in 3dmerge.c to use fake values of dx=dy=dz=1.
* Added -1filter_winsor to 3dmerge.c and edt_filtervol.c.
* Added 'IJK lock' to afni.[ch] and afni_widg.c (Lock menu).
* Added -twopass option to 3dvolreg.c.
04 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -rotcom output to 3dvolreg.c (and hidden -linear option).
* Modified -verbose output of mri_3dalign.c.
01 Sep 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Incorporated changes from Ziad Saad to the Hilbert delay plugin.
* Modified plug_nudge.c to output a 3drotate command line to stderr
when the feeble user presses the new 'Print' button.
* Added call to AFNI_imseq_clearstat() to afni_plugin.c function
PLUTO_dset_redisplay().
24 Aug 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified most places where SESSTRAIL is used to use SESSTRAIL+1,
so that when filenames are shown, they show all the directories
that are shown in the 'Switch Session' dialog. [Per the suggestion
of Florian Hauch, Munich.]
* Also modified afni_pplug_env.c to enable AFNI_SESSTRAIL to be
controlled interactively, and to have it modify the window titles
and session lastnames when AFNI_SESSTRAIL is altered.
22 Aug 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'To Disk?' option to plug_maskave.c for the 'doall' case.
09 Aug 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_floatscan.c to use finitef() on Linux.
* Modified 3dcalc.c to use thd_floatscan() to check results.
* Modified 3dmerge.c to have -1fmask option to restrict filtering,
and -1filter_expr option to do arbitrary linear filtering.
(Also changed editvol.h, edt_checkargv.c, edt_filtervol.c, and
edt_onedset.c)
08 Aug 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Used thd_floatscan() to check/fix possible float errors from
user functions (in the thd_make*.c functions and in afni_fimmer.c).
Was prompted by errors produced in Ziad Saad's Hilbert plugin.
21 Jul 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added AFNI_ENFORCE_ASPECT to afni_pplug_env.c.
* Added AFNI_IMAGE_PGMFILE_[1-9] to afni_splash.c.
20 Jul 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dTagalign.c to write matrix+vector to a file and to
the output dataset header.
* Modified 3drotate.c to read matrix+vector of transformation from
a file or from a dataset header.
17 Jul 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added new program 3dTagalign.c.
* Fixed a bug in the 'Write' callback in plug_tag.c.
12 Jul 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added Left-Right mirror option to afni_graph.[ch] and afni.c to
make graph pixel layout correspond to images if left-is-left.
11 Jul 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 3dZeropad.c.
03 Jul 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 2DChain pseudoplugin.
30 Jun 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Moved plug_environ.c into main afni, on the Misc menu. Modified
places where environment variables are used to allow this
'Edit Environment' feature to work.
* Added '|FFT()|' 1D function to afni.c.
* Created program Xphace.c.
19 Jun 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added ability to set initial string in a 'user-typein' string field
in PLUTO_add_string().
* Created plug_environ.c.
16 Jun 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Tran 2D' to color pbar popup for AFNI controllers.
* Fixed 'Save to PPM' to save a check pattern for the 'none' color.
15 Jun 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added option '-nscale' to 3dcalc.c [that damn Tom Ross again].
* Added an SCO Makefile [from Jason Bacon] and a couple of patches
to go with it.
* Added 'Save to PPM' button to color pbar popup menus, to let the
user save a representation of the color overlay scheme.
* Fixed check_pixmap in pbar.c to be correct in TrueColor.
* Added 'Tran 0D' to color pbar popup for AFNI controllers (but not
for the rendering plugin).
08 Jun 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added new picture to splash screen (the MCW gang). Also, added
AFNI_IMAGE_PGMFILE environment variable to afni_splash.c
23 May 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_idcode.c to use lowercase in dataset IDcodes.
22 May 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added AFNI_USE_THD_open_dataset environment variable to allow
THD_open_one_dataset (in thd_opendset.c) to call THD_open_dataset
instead (in thd_mastery.c), if a '[' is also present in the
dataset pathname.
!!! This feature must be used with care, since some programs !!!
!!! (e.g., 3dbucket) will break if it is used. A program that !!!
!!! writes to a pre-existing dataset MUST NOT open that dataset !!!
!!! with a sub-brick selector list. !!!
19 May 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added changes from Doug Ward for a '-mask' option to 3dNLfim.c.
18 May 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add plug_second_dataset.c and code in afni_graph.c to use it - a
'1D function' that returns the time series from another dataset,
for example to plot the -snfit output of 3dNLfim on top of the
original dataset.
12 May 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Incorporated NLfim changes from Doug Ward, to include calculation
of R**2, per my request.
10 May 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_fimmer.c to print out an error message if nvox is zero.
This happens if the FIM Bkg Thresh is too high. Also modified
afni.c to allow this value to be initialize to 0 (before, 1% was the
minimum).
09 May 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program imcutup.c and function mri_uncat2D.c to break 2D images
up into pieces.
01 May 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_widg.c to disable Datamode->Misc->Version Check if in
realtime mode (due to long hang time while master version web page
is fetched across the network).
* Added program 3dfim+.c from Doug Ward.
28 Apr 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_realtime.c (and afni_plugin.[ch]) to do 'Image Only' realt
ime
acquisition - just show the images, don't do anything else.
21 Apr 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in qsort_floatfloat (cs_sort_ff.c).
* First version of plug_betafit.c.
18 Apr 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Rewrote plug_nudge.c to do rotations and shifts.
* Added mri_copy.c.
16 Apr 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Oops. Added AFNI_SYSTEM_AFNIRC stuff to afni_environ.[ch] as well.
14 Apr 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added options -1Dfile to 3dvolreg.c and plug_volreg.c to save movement
parameters to a 1D file for later ortologizing.
12 Apr 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added AFNI_SYSTEM_AFNIRC environment variable, to allow introduction
of a system wide .afnirc file.
* Added the ability to change datasets in the renderer from script files
(using the saved ID code string). Also, made the threshold slider
change when the script changes the threshold value (forgot this
visual detail before).
11 Apr 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in 3drotate.c when input was a master-ed file. Also added
-clipit option to 3drotate.c.
* Fixed bug in parser_int.c where stdlib.h wasn't included before
drand48() was called.
* Added AFNI_GRAYSCALE_BOT to display.c.
07 Apr 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Included 3dWavelets code from Doug Ward.
04 Apr 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added thd_base64.c routines for dealing with BASE64 encodings.
16 Mar 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -cmask option to 3dmaskdump.c (via new file edt_calcmask.c).
15 Mar 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added AFNI_VIEW_ANAT_BRICK and AFNI_VIEW_FUNC_BRICK environment
variables to afni.c to force switching back to 'view brick'
mode when switching datasets.
* Added '{warp}' string to titlebar when 'Warp Anat on Demand' mode
is engaged.
08 Mar 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added sync() to plug_realtime.c after writing datasets.
07 Mar 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_realtime.c, to reject nzz=1 datasets, print out better
error messages, etc.
* Modified rtfeedme.c to have -nzfake option, for testing the above.
* Modified jp_afni.c to get orientations correct for Signa realtime.
06 Mar 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -sagittal, -coronal switches to 3daxialize.c.
02 Mar 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added plug_nudge.c to move dataset origins around.
* Added -dxorigin (etc.) option to 3drefit.c.
29 Feb 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Revived the program 3ddot.c and added masking options.
14 Feb 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -median and -MAD options to 3dTstat.c (but not to plug_stats.c).
10 Feb 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 3A.: image formats to allow input of unstructured ASCII files
into AFNI programs. Routines changed in mri_read.c and mcw_glob.c.
06 Feb 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added mcw_malloc_sizeof() to mcw_malloc.[ch], to return the size of
of a malloc()-ed region, if possible.
* Added TRUNCATE_IMARR() macro to mrilib.h.
04 Feb 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added IRAN() integer deviate, ERAN() exponential deviate, and LRAN
logistic deviate generators to parser.f
* Added THD_extract_many_series() function, and used in to speed up the
fimfunc work in afni_fimmer.c.
* Fixed error in 3dbuc2fim.c, where stat_aux array was not malloc()-ed
large enough for the EDIT_dset_items() routine usage.
03 Feb 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified GRAN() random number generator in parser.f to make it be
less obviously periodic.
02 Feb 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dvolreg.c to make it not print out the -help stuff when
argc==2.
* Added uran() function to parser.
01 Feb 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added file afni_fimfunc.c, which lets the 'user' add a function to
the FIM+ menu. The Spearman rank correlation is included as a
sample. Also included small changes to afni.[ch], afni_graph.[ch],
and a large-ish addition to afni_fimmer.c.
* Removed useless 'break' statements in afni_graph.c that produced
some annoying 'unreachable code' compilation warnings.
Also modified bbox.c bbox and arrowval utility routines to check
if the input items are NULL before accessing them.
28 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot/plot_x11.c to skip use of XDBE if AFNI_NO_XDBE
environment variable is set.
27 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_sarr.c and thd_get1D.c to speed up (hopefully) reading
of *.1D files.
* Modified afni.[ch] to allow use of '-no1D' option to skip reading
of *.1D files from the dataset directories.
24 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed error in -mask[n] option processing in 3dROIstats.c - that
fiend Tom Ross used argv[narg] instead of argv[narg-1] to check
for the presence of the 'n' option.
20 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Also added a popup error message when floating point errors are
detected in inputs to to3d.c
* Added '1xN' pattern to 24swap.c to allow for nonswapped data.
19 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified to3d.c to count and report number of negative voxels when
the input images are shorts - this is to provide a check for the
need for byte-swapping.
13 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added plug_scatplot.c - scatter plotting. Added PLUTO_scatterplot()
function to afni_plugin.[ch].
* Fixed error in setup of Range choosers in plug_histog.c - they
were initialized to incorrect values.
11 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Replace 'New Stuff' button under the Misc menu with 'Version Check',
which just runs afni_vcheck and puts the output into a popup.
* Modified plug_render.c to make Cutout Overlay work properly with
ShowThru.
10 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_render.c to add AFNI_RENDER_SHOWTHRU_FAC variable to
control the compositing of ShowThru images.
* Added program afni_vcheck.c, to check the AFNI version against the
master copy back at the central AFNI web site.
07 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_render.c to allow ShowThru color overlays: by doing two
renderings - underlay and overlay separately - and then compositing
the two images afterwards.
05 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changed default AFNI_SPLASHTIME to 1.0 seconds in afni.c.
* Added 'static' to mixshade menu strings in plug_render.c.
* Added MCHECK to DBG_SIGNALS in dbtrace.h.
* Added routine mri_write_raw() to mri_write.c.
* Modified from3d.c to have -raw and -float options.
04 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added gran(m,s) function to parser.f and 3dcalc.c.
* Added 'Set All' and 'Set Defaults' buttons to FIM+ menu in afni_graph.[c
h].
* Removed contents of file README.changes.
* Abbreviated 'Cannot find ...' error messages in thd_reconpar.c.
* Added total dataset count report to afni.c input routine.
03 Jan 2000, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3ddata.h to increase maximum number of datasets per directory
to 512 anats and funcs (each), and max number of directorys to 80.
* Modified afni.h, afni_fimmer.c, afni_pcor.c, and afni_graph.c to
add '% From Top' option to FIM menus.
21 Dec 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_render.c to put the 'non-mixing' stuff into a separate
menu on the 'Color' popup.
* Took 3dROIstats.c mods from Mike Beauchamp for the -summary option.
20 Dec 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified parser.f to remove the possibility of divison by zero in
the expression evaluation routines.
* Modified display.[ch] and plug_render.c to allow 'non-mixing' of
colors displayed from rendering results.
14 Dec 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified edt_emptycopy.c, editvol.h, and afni_plugin.c to have newly
created datasets get assigned the same anatomy parent as their
progenitors.
* Modified afni.c so that manually warped datasets become their own
anat parents.
* Modified 3drefit.c to allow SELF and NULL to be valid arguments to
the -apar option.
13 Dec 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added mode functions to parser.f, parser.inc, and 3dcalc.c.
* Added -force option to adwarp.c; otherwise, program will not now
overwrite existing dataset.
* Modified function qginv() in mri_stats.c to never return a value
greater than 13, no matter how absurd the value the user enters.
* Modified edt_dsetitems.c, editvol.h to have a new editing item
ADN_anatpar_idcode - to let a program attach an anat parent idcode
to a file (vs. an anat parent dataset).
* Modified afni_func.c to NOT print out a forced adoption message when
a dataset is set to be its own anatomy parent.
* Modified plug_maskave.c to properly initialize sum=sigma=0 for EACH
separate sub-brick calculation.
09 Dec 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -hilbert option to 1dfft.c, and -install option to 1dplot.c
* Added 0 definition of DBG_trace to dbtrace.h in the case USE_TRACING
is not defined.
08 Dec 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Oops. Took out some debugging statements in 3dTstat.c that somehow
survived until now.
* Modified count of forced adoption potential conflicts in afni_func.c
to avoid some warning messages.
* Added 'NULL' to return in plug_tag.c, where it had been forgotten.
* Added program 1dnorm.c.
* Added -byslice option to 3dDetrend.c.
07 Dec 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 3drename.c, to rename dataset .HEAD and .BRIK files
at the same time.
* Added environment variable to control Winsor21 function in imseq.c.
03 Dec 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Print a warning message in afni_func.c when a forced adoption takes
place.
* Disable 'sides' labels if an environment variable is present.
* Incorporate '-quiet' options in 3dclust.c and 3dROIstats.c from
Mike Beauchamp.
* Incorporate sub-dataset selection for various statistical programs
from Doug Ward.
01 Dec 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c and afni_func.c to turn on XSynchronize if -TRACE
option is used (or when DBG_trace gets set to 2).
* Fixed bug in afni_func.c AFNI_force_adoption() routine: the
PRINT_TRACING output after the dataset scan would crash if no
dataset was found.
* Modified imseq.[ch] and afni.c to set 'sides' strings for an image,
so that 'left=SIDE' can be displayed correctly in any orientation
of the image flipping process.
30 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dTshift.c to allow '-tzero 0.0' and '-slice 0' as
options (I used <= instead of < in the original code).
* Modified plug_render.c to reset func_cmap_set=0 if a render
handle is destroyed - the colormap wasn't being properly
reloaded when a new underlay dataset was selected.
* Modified SHOWOFF handling in afni.c to always show compilation
date no matter what.
29 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -tocx, -fromcx, and -nodetrend options to 1dfft.c.
* Modified quadratic detrending calculation in thd_detrend.c.
* Added -use option to 1dplot.c.
* Added SHOWOFF macro to afni.c, distmake, and Makefile.INCLUDE.
* Got some 3dDeconvolve.c fixes from Doug Ward.
28 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added function ZTONE to parser.f.
25 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 1dcat.c - catenate *.1D files.
24 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 1dfft.c - to calculate abs(FFT(timeseries)).
* Modified 1deval.c to allow input of time series.
* Got some 3dDeconvolve.c changes from Doug Ward.
23 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dcalc.c differential subscripting to allow abbreviations
of the form a+j, a-k, etc.
* Added -quiet option to 3dmaskave.c.
* Added -normalize option to 3dDetrend.c.
* Fixed error in afni_func.c (and adwarp.c) when writing out a dataset
that was told to have a byte order different from the native order -
it was written in native order and the header wouldn't know about
that - the result was the file was read in incorrectly later.
* Also fixed same error in 3daxialize.c.
* Also fixed thd_writedblk.c and thd_loaddblk.c to handle byte swapping
on complex data correctly.
22 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -histpar option to 3dcalc.c.
* Added differential subscripting to 3dcalc.c.
* Modified thd_intlist.c to allow for negative list elements.
18 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified cs_addto_args.c to make the mangling of the arglist
more flexible.
* Used the previous change in afni.c to add the environment variable
AFNI_OPTIONS that will always be added to the command line args.
* Incorporated the OSF1 changes from Matthew Belmonte.
17 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Removed some -help from imcalc.c, since 3dcalc -help has the
same info.
* Added function PARSER_1deval() to parser_int.c.
* Added environment variable AFNI_MARKERS_NOQUAL to afni.c.
* Fixed bug in 3dDetrend when -expr string had no variable symbols.
* Modified thd_iochan.c to use SO_REUSEADDR to help close down
sockets quickly. (But later commented this code out.)
16 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added more -help to 3dTshift.c, per MSB's comments.
* Added cubic detrend routine to thd_detrend.c.
* Added mri_read_1D() to mri_read.c. This adds the ability to
do sub-vector selection, and does the transpose too.
* Added mri_write_1D() to mri_write.c. This just does the
transpose before called mri_write_ascii().
* Modified 1dtranspose.c, 3dcalc.c, waver.c, afni_graph.c, and
model_convgamma*.c to use mri_read_1D().
* Modified afni_graph.c to use mri_write_1D().
* Added program 3dDetrend.c: remove time series trends.
* Added predefined 't' and 'l' to 3dcalc.c.
09 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added function RWC_visibilize_widget() to xutil.[ch] - used to ensure
that popup widgets are fully onscreen. Used this function in
afni_func.c, afni_graph.c, afni_setup.c, bbox.c.
* Added missing 'void' to declaration of function setup_tmpdir() in
thd_http.c.
03 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed the -help output for 3drefit.c, in the description of '-apar'.
02 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dcalc.c to fix problem with using sub-brick selectors of the
form '-b3 zork+orig' -- if zork+orig was a 3D+time dataset, and it
was used as the template for the output, the output would be marked
as 3D+time even though it was not. The solution was to mangle such
inputs to the form 'zork+orig[3]', which already worked fine.
01 Nov 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dclust.c and edt_onedset.c to have a -verbose option, so as to
print out progress report info.
* Added MCW_hotcolor() to xutil.[ch], to get rid of HOTCOLOR macro usage.
* Added function PLUTO_set_butcolor() to afni_plugin.[ch], to let plugin
set its menu button color.
31 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Finished program 3dTshift.c - time shifting.
30 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_detrend.c to have linear and quadratic detrending,
and an L2 normalizing function.
29 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added thd_1Dtodset.c - provides the inverse of thd_dsetto1D.c
(inserts a vector into a dataset time series, rather than extracts it).
* Add thd_detrend.c - detrend a timeseries and provide mean, slope.
28 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Removed 'experimental' message for TrueColor visuals in display.c.
* Added csfft_nextup_one35() function to csfft.c.
* Modified various programs to use csfft_nextup_one35() in place
of csfft_nextup(), for efficiency.
* Moved shifting routines from thd_rot3d.c to thd_shift2.c, so that
they can be used in other programs.
21 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a couple of small bugs in 1deval.c.
20 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified -tim in afni.c to allow for 3D inputs (space-then-time=-zim,
or time-then-space=-tim).
19 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 1dtranspose.c.
* Added option -noijk to 3dmaskdump.c.
* Added option -tim to afni.c - also modified afni.h, afni_graph.[ch], and
afni_func.c to make it work. This option is like -im, but interprets
the images as being spread thru time rather than space.
18 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added history copy to afni_func.c's creation of follower datasets.
* Added -preserve option to 3dfractionize.c, to allow the output dataset
to keep the input values, rather than create a fractional mask.
* Added program 3dmaskdump.c, to dump voxel values out to ASCII.
* Added qsort_int() to mri_percents.c.
14 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added option -apar to 3drefit.c, to allow (re)setting of the anat parent
.
* Added option -warp to 3dfractionize.c, to allow inverse warping from +tl
rc
coords back to +orig coords during the fractionation process.
13 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 3dTstat.c to compute the same stuff that plug_stats.c
does, but in a batch program.
09 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added AFNI_ENFORCE_ASPECT environment variable, to make imseq.c
enforce the image aspect ratio - this is to be used when the
window manager doesn't do this properly.
08 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Increased buffer size in mri_read.c for ASCII file line length.
07 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_makemask.c to include a counting function.
* Modified plug_histog.c to use THD_makemask() rather than create
its own mask the hard way (I just forgot about that routine).
* Added program 1deval.c, to evaluate an expression at a bunch
of points and write it to disk - the goal is to simplify
creation of sample 1D files.
06 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_histog.c and afni_plugin.[ch] to plot extra curves
in histograms.
* Modified coxplot/plot_motif.c to look harder for the HOTCOLOR before
it gives up and uses the default.
05 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in mcw_malloc.c, where it printed out the wrong
info when it found an overwrite error in a malloc()-ed
block of memory.
04 Oct 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added histogram of correlation coefficient to plug_histog.c.
30 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added plug_histog.c (histogram plugin) and a histogram
plotting routine to afni_plugin.c.
28 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added environment variable AFNI_PCOR_DENEPS to afni_pcor.c,
so that user can set the DENEPS test for the correlation
coefficient calculation.
24 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed wcsuffix bugs in afni_graph.c
- didn't mangle output name correctly!
- overwrote the end of the wcsuffix string!
21 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* added message about 3drefit to thd_initdblk.c.
* modified MEDIAN function in parser.f to handle N=3 case separately.
20 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* thd_initdblk.c: print out a warning if byte order is unspecified when
creating a dataset.
* thd_notes.c: add the username to the History Note stamp.
19 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* If dataset header doesn't have BYTEORDER attribute, thd_info.c now print
s
'{assumed}' next to the reported byte order.
* Added hostname to History Note time stamp, so you can see what on what
machine a program was run.
16 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changed THD_open_one_dataset() to THD_open_dataset() in programs
3dFourier.c, 3dROIstats.c, 3dmaskave.c, 3dnvals.c, 3dproject.c, 3dttest
.c.
* Modified 3dclust.c to use -1dindex and -1tindex, as in 3dmerge.c
* Modified 3dTcat.c to have options -rlt+ and -rlt++.
15 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -slices option to 3dmaskave.c.
* Added default values for i,j,k to 3dcalc.c.
* Added thd_makemask.c.
* Added -mask option to 3dpc.c.
14 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added complexscan function to thd_floatscan.c.
* thd_loaddblk.c now scans complex inputs for errors, if requested.
* to3d.c now scans float and complex input images for errors.
* to3d.c now clips out all but a few of the input image files on
the command line for the History Note.
11 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Got History changes from Doug Ward.
08 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified the error messages in some of the thd_*.c files to
be more verbose (Bharat Biswal couldn't understand one).
* Modified afni_fimmer.c (and afni.h, afni_graph.c) to allow computation
of '% From Ave' = percent change computed from the average instead
of from the baseline [per AJ].
01 Sep 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Wrote a Notes viewing/editing plugin.
31 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added a History Note feature to thd_notes.c.
* Added a routine to afni_plugin.c to produce a command string
summary of the inputs to a plugin.
* Modified many programs and plugins to write to the History Note.
30 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_fimmer.c to accept an upper limit on the computable
percent change.
29 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified count.c to accept a '-scale' option.
* Modified Tom Ross's 3dNotes.c software to be a set of routines (thd_note
s.c),
for eventual use in a plugin.
23 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 1/N scaling option to csfft.c. Modifed fftcheck.c accordingly.
19 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -indump option to 3dmaskave.c.
* Added 'Jump to (ijk)' button to image window popup: afni.[ch], afni_widg
.c.
09 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added the radix-5 routine to csfft.c.
* Modified edt_blur.c, thd_rot3d.c, and plug_power.c to use new
FFT abilities.
08 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added the radix-3 routine to csfft.c.
07 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added a '[left is left]' or '[left is right]' label to the winfo text
in AFNI coronal and axial images displays. Affected files
imseq.[ch], afni.c.
* Removed the non-toggle code leftover from the 01,AUG,1999 changes.
06 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_plugin.[ch] to allow plugins to set a sequence code,
which determines the order in which the plugins appear on the menu.
* Received 4 plugins (plug_hemisub, plug_maskcalc, plug_roiedit,
plug_maxima) from the estate of Rick Reynolds.
02 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added the AFNI splash screen; see afni_splash.[ch].
01 Aug 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changed 'Voxel Coords' and 'Show Hints' pushbutton on Misc menu to
toggle buttons. Modified afni.h, afni_widg.c, and afni_func.c.
* Added a 'writeownsize' option to the Misc menu, but then changed
my mind and #ifdef-ed it out.
30 Jul 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program float_scan.c and function thd_floatscan.c to check
floating point files and arrays (respectively) for illegal values
(e.g., NaN and Infinity). Incorporated thd_floatscan() into
thd_loaddblk.c (if AFNI_FLOATSCAN is set).
29 Jul 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed afni_graph.c to not use XComposeStatus in XLookupString call,
which was causing trouble on SunOS.
* Line 2707 of afni_graph.c had an '==' for assignment, instead of '='.
The effect was a possible failure of the x-axis (xax_tsim) graphing
mode. I don't think this failure ever occured in practice.
19 Jul 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in 3dcalc.c, where it tested CALC_type[ids] for > 0, whereas
it should have been >= 0. The effect was that 3D+time byte valued
datasets were not loaded into the atoz array.
14 Jul 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 'Scripts' in plug_render.c to allow save/restore of grafs.
Also modified mcw_graf.[ch].
13 Jul 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Scripts' option to plug_render.c.
07 Jul 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 3dTsmooth.c.
* Modified afni_plugin.c to skip date crosscheck on systems that don't
have the C function strptime().
* Added -vnorm option to 3dpc.c.
17 Jun 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 24swap.c.
15 Jun 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed afni_receive.c to return the proper 'key' value from function
AFNI_receive_init().
* Modifed plug_render.c to redisplay func dataset statistics after
receiving a drawing notice.
* Modified afni_plugin.[ch] to crosscheck each plugin's compilation
date with AFNI's, and print a warning if they differ.
08 Jun 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added MCW_new_idcode() to 3drotate.c -- was producing datasets with
identical idcodes, which is terrible!
* Added function THD_check_idcodes() [thd_checkidc.c] to allow AFNI to
check the idcodes in all datasets for duplicates.
07 Jun 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in edt_onedset.c that always applied zscore transformation
if possible!
* Created afni_environ.[ch], which now process a ***ENVIRONMENT section
of .afnirc. Also, in all programs, switched use of getenv() to
my_getenv(), which just makes sure that .afnirc's ***ENVIRONMENT has
been processed before using getenv(). In this way, the .afnirc setup
will be universal.
04 Jun 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added ***ENVIRONMENT section to .afnirc file processing: changes to
afni_setup.c, and to afni.c to have environment variables setup
before other things.
* Made AFNI_load_defaults() in afni.c look at environment variable
AFNI_name if X11 resource AFNI*name doesn't exist.
03 Jun 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed thd_info.c where it refered to brick labels that might not
exist -- now it uses the DSET_BRICK_LAB macro, which always works.
* Fixed plug_realtime.c to add brick labels to the FIM dataset.
02 Jun 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_render.c to draw partial crosshair sets like the
image viewers.
* Modified afni.c to send a 'process viewpoint' message when the
partial crosshair status changes, so that the renderer will
get a notice and be able to redraw itself promptly.
* Modified plug_realtime.c to use polort.
* Added ability to change FIM background threshold percent (FIM_THR)
to afni_graph.[ch], afni.c, afni_fimmer.c, and plug_realtime.c
30 May 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added a variable polort order to afni.c, afni.h, afni_graph.c,
and afni_fimmer.c.
* Discovered a bug in afni_pcor.c in the % Change calculation,
where the last ort wasn't being used in the baseline estimation.
27 May 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added an X defaults initializer for the graph ggap.
28 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* In 3daxialize.c, made sure that the slice-wise time offsets
are nulled out.
26 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed thd_info.c to report dataset axes dimensions correctly
(also fixed DAXES_NUM macro in 3ddata.h).
* Put code in plug_render.c that allows non-axial datasets to
be rendered -- but disabled it for now.
* New program 3daxialize.c will rewrite a dataset with BRIKs
into the RAI (axial) orientation.
19 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c, afni.h, afni_widg.c to add 'Set All' button
to Lock menu.
15 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read.c to also try ppm from mri_read() function.
* Modified mri_write.c to write byte files as pgm.
* Modified mri_to_rgb.c to have a 1 rgb image -> 3 byte image function,
and fixed a bug in the 3 images -> 1 rgb image function.
* Added mri_dup.c, to upsample a 2D image; added program imupsam.c
to do this function from the command line.
14 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c to fix the pbar_sgn_* initialization, since
it incorrectly checked the thresholds against the range
0..1 rather than -1..1 [per Chad Moritz of UW Madison].
13 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_read.c to allow 3D: hglobal to be < -1 as
long as hglobal+himage >= 0 [per Gary Strangman of MGH].
* Added mri_cut.c, function to cut out a sub-image.
05 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_http.c to allow change of user ident for ftp://
access to files.
* Tested AFNI with LessTif v.0.89 -- seems to work.
03 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_render.c to have the currently active dataset
'selected' when the user popups a new dataset chooser.
* Removed the non-working rotation feature from 3ddup.c.
02 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_http.c to use directory $TMPDIR if defined, rather
than always rely on /tmp.
* Also added routines to this file to allow transfer of 'ftp://'
URLs -- this is done using a shell script running the
ftp program.
01 Apr 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Finally centralized the computation of the '[A]' type labels for
AFNI controllers in afni_func.c, in the new routine
AFNI_controller_label(im3d). Then modified afni_plugin.c,
afni_widg.c, plug_render.c, plug_drawdset.c, and plug_tag.c
to use this function.
31 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_receive.c to allow for new types of transmission
DRAWNOTICE = notification that something was drawn
DSETCHANGE = notification that dataset pointers may have changed
(needed when rescanning sessions)
* afni_receive.c now handles transmission to all the interested
viewers using the AFNI_process_* routines within.
* Modified plug_drawdset.c to properly recover when rescan is used.
* Modified plug_render.c to redraw when DRAWNOTICE is received,
and to recover when rescan is used.
* Modified 3dcalc.c to scale each output sub-brick to shorts/bytes
separately, rather than globally [per request of KMD].
29 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_receive.c and others to allow for multiple receivers
for an IM3D.
* Modified plug_render.c to auto-redraw when it receives notice of a
crosshair location move.
26 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added a FREE_VOLUMES to plug_render.c after a new anatomical
sub-brick is selected.
23 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added call to reload_DC_colordef in imseq.c so that
Save:one works properly after palette adjustment.
22 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added SOLARIS_DIRENT_PATCH code to mcw_glob.c.
12 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed 2 bugs in plug_render.c
- opacity_scale changed wasn't checked if number of cutouts == 0
- didn't invalidate overlay when loading new functional dataset
10 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* In afni_graph.c, added deletion of XImage after XGetImage
is used to save the graph window to a file.
09 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* In refit_MCW_optmenu (bbox.c), found I had to free the av->sval and
->old_sval values, since they were being abandoned.
* Added AFNI_NO_MCW_MALLOC environment variable to mcw_malloc.c,
to let user turn off these routines.
08 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* More changes to mcw_malloc.[ch].
* Added macro FREE_AV() to bbox.h, because I found out that all places
where I used XtFree() on an arrowval would leave the string values
(sval) high and dry.
06 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Removed GNU malloc from afni.c and incorporated my own mcw_malloc.[ch]
functions/macros.
03 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_sarr.c to skip the realpath() expansion if the
environment variable AFNI_NOREALPATH is set.
01 Mar 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added the *_p2t, *_t2p, and *_t2z functions to parser.f, parser_int.c,
and 3dcalc.c.
* Created ASCII PPM file gmove.ppmap to use in gmovie csh script.
* Removed tapering from FFT interpolation in thd_rot3d.c.
25 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added the MEDIAN function to parser.f and 3dcalc.c.
23 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a bug in thd_trusthost.c.
22 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New routine 'addto_args' (addto_args.c) used to catenate stdin
to the (argc,argv) command line of a program. Testbed is
3dRegAna.c (for D. Emge).
* Added 'LOCK_ZORDER' command to plug_realtime (for Vinai).
* Fixed bugs in plug_render.c having to do with the 'Expr > 0' cutout
+ Combination with AND was incorrect (counted ncdone too many times);
+ Test for evaluation to a pure number was incorrect if there were
any leading blanks.
18 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* In plug_render.c
+ Replaced 'Remove Isolas' w/ 'Remove Small Clusters' in plug_render.c
+ Added the slant cut planes.
* In imseq.c, made it so that closing a rowgraph or surfgraph window
turns off the feature.
16 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified bbox.[ch] to allow non-power-of-10 steps in an arrowval,
if the av->fstep structure component is modified by the user.
* Some minor cosmetic changes to plug_render.c.
15 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifed mri_render.c to change the way it deals with color volumes.
* Modified plug_render.c to allow for color overlays.
* Modified xim.c and display.c to deal with converting a RGB image
to an XImage in a more efficient way.
11 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified many routines in mri_*.c to deal with MRI_rgb type
images, in preparation for modifying imseq.c to deal with such.
* Modified display.[ch] to include a 'colordef' for conversion
between Pixel and RGB triples.
* Added routine to xim.c to convert MRI_rgb image to an XImage.
* Changed imseq.c to allow MRI_rgb images.
* Created program 1dplot.c.
10 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Expr > 0' cutout to plug_render.c
* Added SIND(), COSD(), and TAND() functions to parser.f
09 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to imseq.c include putting the colorbar popup menu on
ctrl-Button3 if there is only 1 image in the sequence, and
changing the sharp-factor arrowval to run from 1-9 instead
of 1-99.
* Added 'MCW_noactext' option to arrowvals (bbox.c), so that
the usual actions taken when the user leaves the window
are not taken.
* Added many features to plug_render.c: automation, cutouts,
and accumulation.
* Fixed 3drefit.c -view option.
07 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added new program 3dfractionize.c (per Ziad Saad).
05 Feb 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added plug_render.c, the first version (grayscale only) of the
volume rendering code.
* Changed name of AREN to MREN and put it in mri_render.[ch].
* Cloned the mcw_graf.[ch] routines out of xv.
* Added the coordinate stuff to 3dcalc.c.
30 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Flood->Zero' and 'Zero->Value' options to plug_drawdset.c.
29 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed afni_func.c so that if the user presses 'See Function'
when there is no function, it turns the toggle button back
off. Formerly, it turned off the internal flag, but didn't
change the toggle button state, so that the user was fooled.
27 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add 'UK Flag' location marker to RowGraphs and SurfGraphs.
26 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in initialization and usage of Xdbe library, in coxplot.
25 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Created the 'AREN' routines (aren.[ch]) for volume rendering, on top
of VolPack. Not sure what to do with them yet.
24 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified coxplot (coxplot.h, plot_motif.c, plot_x11.c) to use the
X11 Double Buffer extension, if HAVE_XDBE is defined. This makes
the redrawing of graphs look much smoother.
21 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added SurfGraph feature to imseq.c.
* Added OSfilt9 to imseq.c and the 2D transformations menu (afni.c).
* Modified coxplot/plot_topshell.c to store a handle to the form at top
of the graph window hierarchy.
* Modified xutil.c to add the 'SaveUnder' property to the hints widget.
20 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in mri_stats.c, where 'p2t' conversion was done backwards
for the F statistic (p should have been q, and vice-versa).
19 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added '-1ddum' argument to 3dpc.c.
15 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed the old 3dpc.c to work with the new AFNI data storage,
and to use the EISPACK routines instead of LAPACK (with help
from Vinai Roopchansingh).
* Made swap4 work with float input datasets as well as int.
11 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified the rest of edt_coerce.c and edt_volamax.c to allow doubles.
* Added thd_mastery.c, which allows a dataset to be 'mastered' on input,
so that its bricks are a selection of bricks from a master dataset.
Adds the routine THD_open_dataset(). Modified 3ddata.h and a
bunch of other functions.
* Modified 3dinfo.c, 3dcalc.c, rtfeedme.c, from3d.c, 3drotate.c, and
3dvolreg.c, to use the new opening routine, to allow for subset
selection.
10 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified edt_coerce.c to make EDIT_coerce_type work with doubles.
07 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.c to move placement on screen of the
'Opt->Colors Etc.' submenu if it ends up placed directly over
the 'Opt' menu. This could happen on some versions of Motif
when the graph window is up against the right edge of the
screen. A callback is executed when the submenu is mapped,
and if it is in a bad location, its XmNx value is changed.
06 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.c to try to avoid crashes when graphing window
is closed using 'Opt' menu 'Done' button. Seems to be caused
by Expose events, but what exactly isn't clear -- happens on
SGI systems. Using the 'Done' button now starts a 50 msec timeout
before the 'q' key is simulated. Also, the Expose event count
is now checked before processing, and only if event->count == 0
is any work done. Why these changes do the job is not obvious.
05 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified the way imseq.c places the dialogs (Disp and Mont buttons),
so as to reduce the likelihood that some of the dialog will appear
offscreen.
* Added HorZ ('h') selection to afni_graph.c 'Opt->Grid' submenu, which
will draw a dashed line at the y=0 level in each sub-graph.
04 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed the time lock feature in afni.c so that it would not operate
if toggled off. [Oops]
* Added AFNI_ALWAYS_LOCK environment feature.
03 Jan 1999, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added routine MCW_widget_visible to xutil.c, and used it in imseq.c
and afni_graph.c.
31 Dec 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c crosshairs to allow display only along certain axes.
30 Dec 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added function Winsor9 to the 2D transformations, in imseq.c.
* Added RowGraphs to imseq.c, also affecting plot_ts.c (in coxplot)
and afni.c.
22 Dec 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a bug in plug_volreg.c, where the ax? variables were used
before they were defined, resulting in the wrong order of output
of the estimated movement parameters in the graphs and dfile.
17 Dec 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified xutil.c to use XmChangeColor to change the color
of a widget (routine MCW_set_widget_bg).
* Added some changes by Doug Ward to speed up linear regression
calculations.
16 Dec 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Removed TESTER code from afni_widg.c, and added some STATUS()
printouts to trace progress.
13 Dec 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a bug in the dataset -> time series routines that didn't
scale properly if some of the brick factors were zero and
others were not. Files affected: mri_to_float.c, thd_dsetto1D.c,
thd_fdto1D.c, and thd_initdblk.c.
10 Dec 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added a timeout for the child process in plug_realtime.c.
04 Dec 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added unrolled fft8() to csfft.c.
* Modified thd_rot3d.c to start the FFT size calculation at least
at 95% of the actual width rather than 90%. This reduces the
likelihood of wraparound effects.
03 Dec 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a problem in 3dmerge.c with '-datum float' and the sub-brick
scaling factor, when editing one dataset only.
27 Nov 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed some logical errors in 3dmerge.c with interaction of -1dindex,
-1doall, and the dataset I/O.
23 Nov 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a typo in plug_realtime.c and plug_volreg.c that made the
choice of 'Heptic' use quintic interpolation instead.
20 Nov 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified csfft.c to use unrolled routines for FFTs of length 16,
32, and 64. Also added special routines using the fft64 code
to do lengths 128 and 256.
* Modified mri_3dalign.c and 3dvolreg.c to allow specification of
a different interpolation method to be used at the final
rotation to the output brick.
18 Nov 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a bug in plug_power.c in the untangling of FFT coefficients.
* Modified afni_slice.c to properly clip short and byte interpolation
to avoid overflow.
16 Nov 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_align.c, mri_2dalign.c, and mri_3dalign.c to ensure
that the weighting factors are non-negative.
* Modified 3dvolreg.c to skip registration on the base volume.
* Added plug_volreg.c to do the same job as 3dvolreg.c.
* Fixed bug in 3drotate.c that caused -[ab]shift commands without
directional suffixes to be converted into zeros.
12 Nov 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dmerge.c to have new -1dindex and -1tindex options.
03 Nov 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c, afni_widg.c, and afni.h to allow user to lock time
indexes of controllers, as well as the spatial locations.
01 Nov 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added realtime 3D registration to plug_realtime.c.
* Added quintic interpolation option to thd_rot3d.c and places that use
it (3dvolreg.c, mri_3dalign.c, 3drotate.c, and plug_realtime.c).
26 Oct 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Finished plug_tag.c, and added tagset to a 3D dset. Modified afni.c
to allow markers panel to open when there are no markers, so user can
control the color of the tags.
* Modified mri_max.c to fix the initial values.
* Modified 3dvolreg.c and mri_3dalign.c to add a clipping option.
21 Oct 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added routines to afni_plugin.c to create/manipulate PLUGIN_strval's
[= label + textfield].
16 Oct 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Released 3dvolreg.c to Tom Ross for beta testing.
09 Oct 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modifed afni.c and thd_fdbrick.c to allow the user to control the
image flipping -- that is, to let left be displayed on the left.
01 Oct 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified mri_rota_shear to double up on FFTs -- speeds it up by
about 30%.
* Modified mri_align.c and mri_2dalign.c to allow choice of
interpolation method at each stage of registration.
* Modified imrotate.c, imreg.c, and plug_realtime.c to use the new
image alignment methods.
29 Sep 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added routine mri_rota_shear() to mri_rota.c to do 2D image rotation
using the Paeth shearing method combined with FFTs.
28 Sep 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified edt_onedset.c to correctly deal with clipping a dataset
when the clip range is larger than the dataset range, and the
datum type is short.
22 Sep 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program 3dTcat.c, to catenate multiple 3D+time datasets into
one big dataset (and possibly detrend them at the same time).
This was adapted from 3dbucket.c
18 Sep 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program cdf.c to provide a command line way to get results
from the 't2p', 'p2t', and 't2z' routines.
* Modified afni_setup.c so that when a .pal file is input, the
last newly defined palette becomes the active one in the
AFNI controller which read the file in.
17 Sep 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added '-1zscore' option to 3dmerge.c (via edt_onedset.c, etc.).
* Also completed the list of 'p2t' and 't2p' routines, as well
as adding 't2z' routines, in mri_stats.c and thd_statpval.c.
16 Sep 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dmaskave.c to allow selection of dataset sub-brick and
dataset value range.
14 Sep 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added '-install' option to afni.c to allow installation of a
new X11 Colormap. Also affected display.[ch], afni_widg.c,
imseq.c, afni_graph.c, xutil.[ch], afni_plugin.c, to3d.c,
and plug_drawdset.c.
* Added '-2swap' and '-4swap' options to to3d.c, to allow data
to be byte-swapped on input. Also added a 'Byte Swap' button
to do the same thing interactively.
09 Sep 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_sarr.c to add routine to 'normalize' a list of
files using the C library routine 'realpath' and to cast out
duplicate files.
* Used this in afni.c and thd_get1D.c.
* Also added *.1Dv files to list of allowable 1D extensions in
thd_get1D.c.
* Doug Ward provided me with the new 3dDeconvolve.c program, as
well as some changes to 2dImReg and 3dRegAna.
25 Aug 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_pcor.c change of 15,JUL,1998 to check denominator
vs. DENEPS rather than 0.0.
23 Aug 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified dbtrace.h and most afni_*.c files to allow not only
debug tracing of routine entry/exit, but also the printout
of other debugging information that was formerly hidden
behind '#ifdef AFNI_DEBUG'.
* A few more changes to make xim.c work properly with depth=24,
which can be either 3 or 4 bytes/pixel.
22 Aug 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified display.c to support TrueColor visuals, and xim.c to
support arbitrary byte ordering, plus 3 and 4 bytes/pixel.
17 Aug 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Adapted old Fortran PLOTPAK to in-memory plotting, with routines
to graph to screen and to PostScript.
* Used this to implement the 'Plot' button in the timeseries chooser,
and to do graphing of the realtime 2D motion parameters.
07 Aug 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified display.[ch] to store extra information about the X11
visual. This isn't used yet, but is preparatory to allowing
support for using TrueColor visuals and installed colormaps.
06 Aug 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added changes to thd_compress.[ch] made by Craig Stark/Paul Reber
of UCSD, to allow them to use their custom decompression
program 'brikcomp'.
* Added realtime 2D registration to plug_realtime.c.
* Modified 3dmaskave.c and plug_maskave.c to allow user to choose
a sub-brick of the mask dataset. plug_maskave.c also now lets
the user save the mask average of a 3D+time dataset into the
timeseries library (for use as a FIM, for example). Also
fixed an overflow bug in both programs when the mask range
is too big for a short or byte dataset.
01 Aug 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added copyright information to some .c and .h files.
* Modified mri_to_short.c to allow for special case of scale!=1.0.
* Modified plug_realtime.c to allow for 2D image alignment.
(Continuation of work from,APR,that was unfinished then.)
First cut is to do all registration at end of acquisition.
* Turned off 'frivolities' during a real-time run.
* Added the ability to graph points+lines together in afni_graph.c
(also see changes of 09,JAN,1998).
27 Jul 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a bug in routine suck_file in afni_setup.c, which put the
terminating NUL character 1 place too far in the output array.
* Wrote program uncomment.c, to remove comments from C files.
* Added model_convgamma2a.c.
* Modified NLfit.c to generate a fixed set of random samples instead
of starting over for each voxel. Also fixed the algorithm that
keeps the best random samples -- it was not always keeping the
best one, just some of them.
22 Jul 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added routine THD_timeof_vox to thd_timeof.c. This allows
computation of voxel time from voxel index, rather than voxel
coordinate.
* Removed some redundant code from 3dTSgen.c -- it opened the
input dataset twice in a row, and loaded the datablock when
there was no need.
* Modified 3dTSgen.c, 3dNLfim.c, and plug_nlfit.c to have new '-inTR'
option to allow computation of model functions with TR set from
the input dataset rather than fixed at TR=1. Note that if the
units of the dataset time axis are msec, they will be converted
to sec instead (allowing msec to be used as a unit was a mistake).
21 Jul 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added model_convgamma.c to represent a gamma variate convolved
with a reference time series. The 'k' parameter of Doug Ward's
model_gammaver.c was modified to be called 'amp' here, since the
impulse response is reparameterized to have peak value = 'amp',
rather than 'k * (rb/e)**r', which is clumsy.
* Modified Doug Ward's NLfit_model.h to ensure that certain routines
needed by model functions can be forced to be loaded.
* Modified 3dTSgen.c to make the '-ncnstr' and '-scnstr' options
recognized, since there is a typo in the manual.
* Modified Makefile.INCLUDE for 3dTSgen and 3dNLfim to use the
proper dynamic linking load flags $(PLFLAGS), and also to include
the proper dependencies.
17 Jul 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added program imstack.c to stack up a bunch of 2D images into
the stupid MGH format. [For Kathleen Marie Donahue.]
15 Jul 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Change afni_pcor.c to remove use of DENEPS test for division
in computation of correlation coefficient.
14 Jul 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added option -skip_afnirc to allow .afnirc file to be skipped.
* Fixed bug in afni_setup.c that didn't manage the palette chooser
menu when starting with 0 palettes and then later reading in some.
* Fixed bug in plug_copy.c that put the anat type off by 1. Also
made the 'Zero [One]' option not make the anat type always be omri.
* Fixed bug in parser.f, whereby the vector versions of the boolean
functions (or, and, mofn) were evaluated incorrectly.
13 Jul 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Incorporated Doug Ward's erosion+dilation routines into the
clustering modules.
09 Jun 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified edt_clust*.c routines to implement -1clust_order option.
* Modified 3drefit.c to have -nowarp option.
05 Jun 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dnoise.c to have option to set noise level on command
line, rather than compute it.
03 Jun 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified AFNI_make_descendants to allow descendancy to flow
from +acpc datasets, not just from +orig datasets.
However, this doesn't work just yet, due to warping issues.
04 May 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added routine THD_purge_one_brick to thd_purgedblk.c, to allow
freeing of one sub-brick from a malloc-ed dataset. Also
defined macro DSET_unload_one(dset,iv).
01 May 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed plug_rename.c to work with compressed datasets. Added a
routine COMPRESS_add_suffix to thd_compress.c to facilitate this.
30 Apr 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dcalc.c to purge dset sub-bricks when finished with them,
and to allocate output buffer sub-bricks only when needed. This is
to keep memory usage down when using compressed 3D+time datasets.
* Also added the -verbose option to 3dcalc.c.
29 Apr 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* At the behest of Ted DeYoe, modified 3dcalc.c to allow operations
on bucket and other multi-brick datasets that aren't 3D+time.
* Also modified 3drefit.c to allow conversion of 3D+time into a bucket.
* This also required the ability to erase datablock attributes, since
they are persistent -- even if the data in the dataset is voided,
the attribute will remain to be written to disk. So a routine
THD_erase_one_atr was added. In files thd_writedset.c and
thd_writdblk.c, every attribute that DOESN'T get written now gets
erased. This will still leave extra attributes (perhaps added by
a plugin) being persistent, but avoids attribute 'hangover' problem.
25 Apr 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified thd_*.c to store byte order (for short and int dsets) in the
.HEAD file. Then when the file is read in, it will be byte swapped
if necessary (which will force it to be malloc-ed, not mmap-ed).
* Also modified 3drefit to allow a byte order to be written to .HEAD
files. Note that this does not affect the .BRIK file.
* Added new environment variable AFNI_BYTEORDER to control byte order
of output datasets. This can be 'LSB_FIRST' or 'MSB_FIRST'. If not
present, this means to use the native order of the CPU.
* Added enviroment variable 'AFNI_NOMMAP' to allow suppression of mmap.
If the value is 'YES', then all datasets will be malloc-ed.
* Modified the 'Purge Memory' button to purge ALL datasets from memory.
Formerly, it only purged the unused ones.
17 Apr 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dcalc.c to allow input of *.1D time series
in place of datasets.
24 Mar 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified plug_copy.c to allow creation of a 1 sub-brick zero-filled
'copy' -- useful for making mask datasets.
* Modified 3dnoise.c for 3D+time datasets, so that a voxel is zeroed
only if a majority of time points at that location fall below
the cutoff.
* Modified plug_drawdset.c to recompute statistics after each edit,
no matter what. Also changed the help message a little.
* Wrote plug_maskave.c to do pretty much the same thing as 3dmaskave.c.
21 Mar 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3dmaskave to allow dumping of all voxels hit by the
mask, and to compute the standard deviation also.
20 Mar 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed EDIT_add_bricklist -- the brick auxiliary data additions
would free data that hadn't been allocated.
* Modified stuff so that Dummy dataset is not deleted -- this
seems to help. (It only takes up 64K, so the loss is small.)
18 Mar 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Made 'ptr' a byte variable rather than char in XImage_to_mri
(xim.c) -- this seems to fix a problem on some machines.
16 Mar 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added internal globbing to 'afni -im'.
* Modified function AFNI_follower_dataset (afni_func.c) to copy
datablock auxiliary data from the data parent, if available.
* Modified 3drefit.c to allow -fbuc and -abuc to work no matter
how many sub-bricks are present.
* Added program 3dmaskave.c to print out averages from dataset
sub-bricks, with ROI selected by a mask.
13 Feb 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Released drawing plugin to MCW users. Includes open and closed
curves, filling, and undo.
* Also added .BRIK output compression to thd_compress.[ch], and to
thd_writedblk.c.
08 Feb 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.c to display dataset indices in graph window,
rather than FD_brick indices. (See the DONT_MANGLE_XYZ location.)
* Modified imseq.[ch], afni_graph.[ch], afni.[ch], and the new
file afni_receive.c to allow transmission of mouse Button2
data to a calling routine. Work is in progress -- more later.
04 Feb 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified dbtrace.h to enable tracing with usual afni run. This
can be turned on/off using the 'Misc' menu, or the '-trace'
option (if the program is compiled with USE_TRACING).
03 Feb 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Also put editvol.c into 'edt_*.c' routines, and thence into
librmi.a
* Added an 'Autoscale' button to graph Opt menu, and also execute
the autoscale code when the graph is 1st drawn.
02 Feb 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed a typo in plug_imreg.c to make the 'Fine Blur' parameter
scale to FWHM properly.
* Broke 3ddata.c into 'thd_*.c' routines, and incorporated them
into libmri.a. Also incorporated 3dmaker.c and iochan.c.
Files 3ddata.c, 3dmaker.[ch], and iochan.[ch] are no more!
01 Feb 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified 3ddata.c to avoid use of 'scandir' routine, which caused
no end of trouble on Solaris.
* Moved the 'mcw_glob' routines into libmri.a. These are used to
get filenames from the directory now.
16 Jan 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Percent Change' calculation to afni_fimmer.c, and
removed the 'real-time' update feature from those routines.
14 Jan 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified symbol for current time index in afni_graph.c, so
that when data is graphed with points the current point
can be distinguished from the graph points.
12 Jan 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Allow a gap between the sub-graph boxes. This is chosen
from the 'Colors etc.' menu.
* Raoqiong Tong fixed a bug in the new parser.f with the
AND, OR, and MOFN functions.
09 Jan 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni_graph.[ch] to allow choice of a timeseries to
be used to define the x-axis graphing. Thus, if x(t) is
the x-axis timeseries, and yij(t) are the data timeseries,
then each graph ij now shows x(t) vs. yij(t) rather than
t vs. yij(t).
* Also modified the Button 1 press in the central graph to
jump to the time index point whose graph point is closest
to the button click.
* Also allowed data plots to be shown as points instead of
lines. 'Points' are drawn using the '_circle' routine
('filled' or 'hollow', as the line is 'thick' or 'thin').
08 Jan 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified scaling for output of 3dmerge.c so that the program
detects if all the inputs are integer types (byte or short,
unscaled). If they are, and the merger type is consistent
with integer type, then the output will be unscaled, otherwise
it will be scaled by a float.
07 Jan 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added a routine to editvol.c to do local averaging of a
dataset faster than -1filter_mean -- it seems to run
about 6 times faster. This is implemented as
-1filter_aver in 3dmerge, so that the older one is
still available. Also modified plug_edit.c to add
this option to the Filter menu.
05 Jan 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'New Stuff' entry to Misc menu, which just pops up
the README.changes file into a readonly text window.
* Program 'quotize.c' will take a text file and make it
into a C array of strings, one line per element. This
is used in afni_func.c to popup the README.changes file,
which is put into the file 'newstuff.hhh' by quotize and
in the Makefile.INCLUDE.
02 Jan 1998, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added ability to read compressed .BRIK files to 3ddata.c
(gzip -d, bzip2 -d, and uncompress are supported).
* Added program '3dnoise' to zero out noise-like regions
of nonnegative short datasets.
* Modified display of dataset names to include number of
points in a 3D+t dataset, and to include a 'z' flag
to indicate compression of dataset.
26 Dec 1997, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fixed bug in palette write-out (afni_setup.c).
* Added a scrollable text output utility (xutil.c). Made
the plugin help use it if the help string has many
lines (afni_plugin.c). Added a line counting routine
to 3ddata.c
22 Dec 1997, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Removed auto-change of threshold scale for bucket datasets
from afni.c. Also unmanages/remanages this scale when
the pbar is being changed, due to horrible visual effects
on the SGI machine nimloth (if FIX_SCALE_SIZE_PROBLEM
is defined).
* Modified pbar.c to store the summed pane heights, and then
recompute the value/label only when such a summed height
changes. This prevents the modification of the value/label
pairs at other panes when resizing only one pane.
* Modified AFNI_bucket_label_CB (afni_func.c) to put the
sub-brick index at the left of the option menu label.
21 Dec 1997, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added ability to read in palettes and colors from .afnirc file,
and interactively from a user-specified file. Also allow
user to reset the top and spacings on the color pbar.
* Modified display.[ch] to put all overlay stuff into a shared
struct for all MCW_DCs. This means that the -unique option
will only generate new grayscale colorcells for each controller,
but they will now share overlay colors. This is intended to
prevent a problem when users add new colors dynamically
from external palette files. This change affected files
afni_func.c afni_graph.c afni_graph.h afni_setup.c xim.c
afni_widg.c bbox.c display.c display.h imseq.c pbar.c
* Modified pbar.c to keep the input pval's exactly when calling
alter_MCW_pbar -- formerly, after resizing the panes, the
values might be altered slightly.
* Discovered that 17,DEC,97 change to AFNI_set_viewpoint could
make graph not be drawn correctly on startup. Added
'never_drawn' variable to graphs and imseqs to allow
this condition to be detected.
18 Dec 1997, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added -noqual option to AFNI to make it skip quality checks
when doing marker transformations.
* Added -view option to 3drefit to let it change coordinate
systems.
17 Dec 1997, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified AFNI_set_viewpoint to skip graph redraw unless
REDISPLAY_ALL or unless a new (x,y,z) location is set.
* Added menu to the pbar label to allow modification of
the colors and spacings.
* Modified display.h to allocate overlay colors from
read-write cells. This allows the colors to be
redefined.
15 Dec 1997, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added 'Compute FIM+' to FIM menu. This saves the best
time series index in a new sub-brick.
* Added some macros to editvol.h to make changing sub-brick
auxiliary values simpler.
13 Dec 1997, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added new file '3dmaker.c', for routines that make new
3D datasets from other datasets. Moved the guts of
the PLUTO_4D_to_typed_* routines into this file.
* Also fixed a 'float *' inside mallocs to be 'float'
in a couple of places in these routines. This should
be innocuous, since most CPUs satisfy
sizeof(float) <= sizeof(float *)
09 Dec 1997, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added a new chooser to let user pick interpolation method
for threshold (statistical) sub-bricks.
* Fixed CUBIC_CLIP in afni_warp.c -- it was incorrectly
placed before the brick_fac scaling, not after.
* Removed FIM menu from Define Function control panel.
30 Nov 1997, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Added the 'bucket' types (anat and func) to 3ddata.h, and
then modified afni, editvol, etc., to utilize this type