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
---- log of AFNI updates (most recent first) ----
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)
An R program that runs independent component analysis in AFNI.
This testing program for ICA only takes one dataset that presumably has
already been properly pre-processed. See more details on:
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 that runs linear mixed-effects analysis at group level in AFNI.
See more details on: 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)
An AFNI program that runs 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 were made 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 were made to avoid statistics inflation for
general linear contrasts when coefficients don't add up to 0.
See more details on: 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_d