AFNI HISTORY
level 1 and higher
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 : afni_history -html -reverse -min_level 1 -past_years 1
---- log of AFNI updates (most recent first) ----
24 Nov 2009, ZS Saad, afni-matlab, level 2 (MINOR), type 4 (BUG_FIX)
Stopped writing empty attributes which caused trouble in AFNI.
Empty attributes make AFNI halt the parsing of the header.
24 Nov 2009, RW Cox, thd_atr.c, level 1 (MICRO), type 4 (BUG_FIX)
Allow 'count = 0' in attributes
Formerly was a fatal error. Now just skips to next attribute. For
Ziad.
23 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Workaround for connection drop between AFNI and SUMA in Shared Memory Mode.
Env SUMA_AttemptTalkRecover allows SUMA to recover from drop.
This ENV is set by default to No.
23 Nov 2009, ZS Saad, afni, level 1 (MICRO), type 4 (BUG_FIX)
A couple of small fixes to drive_switch functions.
The problem with with sscanf reading past string endin certain cases.
23 Nov 2009, RW Cox, 3dmaskSVD, level 1 (MICRO), type 2 (NEW_OPT)
Add -bpass option
23 Nov 2009, RW Cox, 3dTcorrMap, level 1 (MICRO), type 2 (NEW_OPT)
Add various options in the last few days
* -seed = a different dataset for the seed time series
* -bpass = instead of -polort
* -Gblur = blurring
* -Mseed = extra smoothing around the seed
* -Hist = output the histogram of the correlations
23 Nov 2009, G Chen, 3dKS.R, level 2 (MINOR), type 1 (NEW_PROG)
Kolmogorov-Smirnov test
This is an R program that runs Kolmogrov-Smirnov test between
two groups of subjects. It takes individual sub-brick files from
each subject as input and spills two sub-bricks in the output,
first one being the Kolmogorov-Smirnov statistic D, while the 2nd
the corresponding Z-score.
20 Nov 2009, DR Glen, 3dAutomask, level 2 (MINOR), type 2 (NEW_OPT)
apply_prefix option to save automasked input
avoids 3dcalc step that is usually used to apply an automask.
19 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed recorder lag on OS X machines.
On OS X platforms, the 'r' or 'R' recording modes
used to record the previous image it seems.
18 Nov 2009, RW Cox, mri_read.c, level 1 (MICRO), type 0 (GENERAL)
Fix Ziad's stupid error printout in reading .1D files
To indicate which file is causing the trouble.
To limit the number of such Failure messages to a reasonable level.
Sheesh.
17 Nov 2009, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
SUMA now handles labeled datatets in a special manner
An example of a labeled dataset would be FreeSurfer's annotation files.
If an annotation file is present in the spec file (@SUMA_Make_Spec_FS),
SUMA will display it as part of the background.
You can chose to display the labeled dataset in color, contours, or both.
Data from labeled datasets is now shown under the 'Lbl' field in the
surface controller's Xhair block.
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_AlwaysAssignSurface (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_LabelDsetOpacity (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ConvexityDsetOpacity (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ShowLabelDsetAtStartup (see suma -environment for details)
17 Nov 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT)
Option -label_dset creates a labeled dataset from ROIs.
Labeled datasets are now rendered in a special manner in SUMA
17 Nov 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
Option -dset creates a labeled dataset from annotation file.
Labeled datasets are now rendered in a special manner in SUMA
17 Nov 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Script now automatically sets up the spec file with labeled datasets
Labeled datasets are created from annotation files,
and are now rendered in a special manner in SUMA
17 Nov 2009, RW Cox, 3dTfitter, level 1 (MICRO), type 0 (GENERAL)
Let FALTUNG kernel be longer that N/2
Also add synonyms '-L2' and '-L1'
16 Nov 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
allow motion censoring with varying run lengths
Also, if a max is applied in scaling, explicitly limit to [0,max].
16 Nov 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY)
allow motion censoring with varying run lengths
09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added options to check for, and correct 'bowties' in pathches.
Bowties in patches result in non 2-manifold stiched surfaces whose
volume cannot be caluclated. The *bowtie option deal with such cases.
09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added options to shrink patch contours at nodes not in selected nodes.
See options -adjust_contour for details.
09 Nov 2009, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT)
Added option for improved node volume estimation.
The new measure, called node_volg, uses Gauss' Theorem to estimate
the volume associated with a node in two isotopic surfaces. This option
is more robust to surface curvature variations.
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, ZS Saad, MapIcosahedron, level 1 (MICRO), type 5 (MODIFY)
Minor code change, EdgeList was computed twice for no reason.
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.
auto-generated by afni_history on Nov 24 2009