AFNI HISTORY
level 1 and higher
The levels of importance go from 1 to 5, with meanings:
1 - users would not care
2 - of little importance, though some users might care
3 - fairly important
4 - a big change or new program
5 - IMPORTANT: we expect users to know
generated via the command : afni_history -html -reverse -min_level 1 -past_years 1
---- log of AFNI updates (most recent first) ----
30 May 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
AFNI_OVERRIDE_VIEW lets you force all datasets into one view
Should be set to TLRC or ORIG
24 May 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT)
Add -noneg option, to crush negative values in input datasets.
22 May 2013, RW Cox, 3dUnifize, level 1 (MICRO), type 5 (MODIFY)
Change default clip fraction for automask to 0.1 from 0.5
For Juen -- to deal with heavily faded images.
17 May 2013, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE)
added -f to curl, so that failures propagate to $status
14 May 2013, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
New -plusminus option
'Meet-in-the-middle' matching: base(x-dis(x)) = source(x+dis(x)).
For application to unwarping blip-up and blip-down EPI datasets.
Also, fix bug when -no?dis options are used -- when the code for
parameter sub-vector mapping was moved around, the 'free' call to get
rid of any old mapping wasn't moved with it -- bad Bob, bad bad bad.
14 May 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -show_argmin/max
14 May 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
motion file renamed
Renamed motion files for -save_vr without -epi2anat
13 May 2013, RC Reynolds, @RenamePange, level 2 (MINOR), type 4 (BUG_FIX)
added -column to count commands writing listfile
There is a 4096 byte limit in addto_args(), which could be made dynamic.
10 May 2013, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
named glob functions as afni_*; R was using sys funcs, rather than local
09 May 2013, ZS Saad, R_io, level 2 (MINOR), type 4 (BUG_FIX)
Temporary fix of segfault happening in R from R_io.so
Source of problem is a call to COMPRESS_setup_programs()
Not sure why the following crash was happening:
*** caught segfault ***
address 0x3800000100, cause 'memory not mapped'
However a temporary env. SKIP_COMPRESS_SETUP will get around it.
09 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -write_3dD_script and -write_3dD_prefix
08 May 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -rank, -rank_style, -reverse_rank
07 May 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT)
Add -Qfinal option (experimental)
07 May 2013, DR Glen, 3dAnatNudge, level 2 (MINOR), type 5 (MODIFY)
always produce output with -prefix even if no shift
06 May 2013, RW Cox, 3dNwarpApply, level 1 (MICRO), type 2 (NEW_OPT)
Add -short option == save results as shorts
For use in warping label datasets.
06 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added -regress_anaticor example; opt implies -mask_segment_anat/_erode
06 May 2013, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
added option -slice_timing
06 May 2013, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added option -transpose_write
03 May 2013, RW Cox, thd_compress.c, level 1 (MICRO), type 5 (MODIFY)
Substitute pigz for gzip and pbzip2 for bzip2 if present in path
03 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -regress_anaticor and -mask_segment_erode
Use the -regress_anaticor option to regress the WMeLocal time series.
This is the ANATICOR method of HJ Jo.
01 May 2013, RW Cox, 3dQwarp, level 2 (MINOR), type 5 (MODIFY)
Minor updates
Make -emask work with -duplo.
Add SAMPLE USAGE section to help to show how to combine 3dAllineate with
3dQwarp, and/or align_epi_anat.py also.
Add -base and -source options, to make program look more like 3dAllineate.
01 May 2013, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 6 (ENHANCE)
added -help example for -show_trs_uncensored
29 Apr 2013, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 6 (ENHANCE)
set AFNI_NO_OBLIQUE_WARNING in scripts
26 Apr 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 5 (MODIFY)
Make -emask option work correctly with -duplo
26 Apr 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_trs_censored/_uncensored (mostly for X-matrix datasets)
25 Apr 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
strlist chooser stays in same place if re-opened - for Allison
24 Apr 2013, RC Reynolds, @move.to.series.dirs, level 2 (MINOR), type 1 (NEW_PROG)
partition a list of DICOM files by series number
Done for I Shapira.
24 Apr 2013, RC Reynolds, @2dwarper.Allin, level 2 (MINOR), type 4 (BUG_FIX)
did not set 'ver' before goto START
Thanks to I Schwabacher for noting the problem and fix.
24 Apr 2013, RC Reynolds, 3dinfo, level 2 (MINOR), type 4 (BUG_FIX)
allow -space for nifti; actually exit if -view and result exists
Thanks to I Schwabacher for noting the problem and fix.
24 Apr 2013, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -censor_next_TR
Sticking with backward diff for deriv, as it makes sense for censoring.
23 Apr 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added eroded ROIs for -regress_ROI: WMe, GMe, CSFe
22 Apr 2013, ZS Saad, 3dAutoTcorrelate, level 2 (MINOR), type 2 (NEW_OPT)
Added -out1D option to output correlations in text format.
22 Apr 2013, RW Cox, 3dNwarpAdjust, level 2 (MINOR), type 1 (NEW_PROG)
For template-building via @toMNI_Qwarp
Computes the mean warp, and adjusts the individual warps to get rid of
this mean warp (under the presumption that it is some kind of bias).
22 Apr 2013, RC Reynolds, auto_warp.py, level 2 (MINOR), type 0 (GENERAL)
modified afni_base.afni_name.new() with 2 cases of parse_pref=1
This is currently the only application of that parameter.
19 Apr 2013, DR Glen, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
lpi xyz output option
18 Apr 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX)
-useweight didn't actually do anything inside OpenMP
Obviously, this can't be my fault. I blame evil spirits.
17 Apr 2013, RC Reynolds, 3dAFNItoNIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixed old use of use of strcat() after strdup()
Thanks to B Benson and J Stoddard for noting the problem.
17 Apr 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
save_vr result causes crash
16 Apr 2013, RC Reynolds, 3dmaxima, level 2 (MINOR), type 4 (BUG_FIX)
modernize dataset coordinate reporting, using proper signs
Thanks to G Pagnoni for reporting the issue.
16 Apr 2013, RC Reynolds, 3dmaskave, level 2 (MINOR), type 2 (NEW_OPT)
added -sumsq (sum squares) and -enorm (Euclidean norm) options
15 Apr 2013, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
added RESTING STATE NOTE to help
15 Apr 2013, RC Reynolds, 3dSurf2Vol, level 1 (MICRO), type 4 (BUG_FIX)
fixed crash when a surface was not found (struct init)
Thanks to H Yang for noting the problem.
12 Apr 2013, RW Cox, 3dLocalHistog, level 2 (MINOR), type 1 (NEW_PROG)
Collecting counts of labels in nbhd of each voxel
For building atlases that allow for uncertainty in position
12 Apr 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
detach from terminal and graph fading are now the defaults
09 Apr 2013, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT)
Added options for providing orts for each input time series
See options -*_orts in the help output.
09 Apr 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed computed fitts for REML case (was from 3dDeconvolve)
Thanks to G Pagnoni for noting the problem.
05 Apr 2013, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
added Help web link to class handouts
05 Apr 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
revert -save_orig_skullstrip to -save_skullstrip
This should have no effect on results, except for rename of anat_strip
to anat_ns. It also gets around a temporary name change from AEA.py.
04 Apr 2013, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add -Apair option
For testing differences in correlations in 1 group from 2 different
seeds -- the regular seed minus the 'Apair' seed. Also changes to AFNI
to set the Apair seed, etc.
02 Apr 2013, RW Cox, Nwarp, level 1 (MICRO), type 0 (GENERAL)
Replace sqrt(nwarp) algorithm
Schulz method gives unpleasant ringing artifacts in the square root.
Use the Denman-Beavers methods instead, which is slower and maybe a
little less accurate, but doesn't do the ringing weirdness.
01 Apr 2013, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
AFNIio.R's newid.AFNI() was duplicated and the more compact one was broken
01 Apr 2013, ZS Saad, 3dAutoTcorrelate, level 1 (MICRO), type 2 (NEW_OPT)
Added option -mask_source
01 Apr 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
motion file renamed
Some output files like the motion files were accidentally renamed.
29 Mar 2013, DR Glen, general compression, level 2 (MINOR), type 3 (NEW_ENV)
pigz for faster gzip-like compressionpigz is a gzip utility that makes use of multiple CPU's.
It produces and uses .gz files. To use, set AFNI_COMPRESSOR to PIGZ.
28 Mar 2013, ZS Saad, @RetinoProc, level 1 (MICRO), type 4 (BUG_FIX)
Parsing of -on* and -off* options failed for non-integral values
27 Mar 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_group_labels, -label_prefix_keep/_drop
Option -label_prefix_drop can be used to remove bandpass regs for 3dRSFC.
27 Mar 2013, DR Glen, 3dBrickStat, level 2 (MINOR), type 2 (NEW_OPT)
absolute value of voxels for statistics
26 Mar 2013, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Added option -inflate for automatic creation of semi-inflated surfaces
See @SUMA_Make_Spec_FS -help for details
26 Mar 2013, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Loop variable error in 3DEdge/src/convert.c variable s32buf
Affected regions in some locations under: case UCHAR and case SSHORT
26 Mar 2013, ZS Saad, suma, level 1 (MICRO), type 5 (MODIFY)
AlignToExperiment transforms no longer applied to spherical surfaces
This makes spheres show up better by default in SUMA for prying.
26 Mar 2013, ZS Saad, SurfSmooth, level 1 (MICRO), type 2 (NEW_OPT)
Added -match_center to force recentering of smoothed surfaces.
SurfSmooth -help for details
26 Mar 2013, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT)
Add option -cmeth (MEAN or MEDIAN) for Steve Gotts
26 Mar 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Minor changes to Fade feature in graph viewer
Toggle button in Opt menu.
AFNI_GRAPH_FADE environment variable.
Make sure it works with Clusterize and InstaCorr updates.
25 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Merged handling of CoordBias with Prying, all in VisX
Lots of annoying little details there. See functions like:
SUMA_*CoordBias*, SUMA_ApplyVisXform(), and SUMA_Apply_VisX_Chain()
25 Mar 2013, P Taylor, 3dReHo, level 2 (MINOR), type 2 (NEW_OPT)
More voxelwise neighborhood shapes available.
Voxelwise neighborhoods can be any sphere/radius size, and even
ellipsoidal. Some memory stuff should be better as well.
22 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added stippling for line segments DOs, see SUMA's ctrl+h for details.
22 Mar 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Fading of graph sub-windows with the 'F' key
20 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Texture demos in DriveSuma were failing.
Problem was a combination of coordinate clipping when frame coords
were at 0 or 1. That is now fixed. Also, demo.*do files needed changing
to move texture on surface into mobile.niml.do
Depth test is no longer disabled with textures.
20 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Text was not appearing at times. Bug was in SUMA_SO_NIDO_Node_Texture()
19 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Prying was off for new GIFTI standard-mesh surfaces.
Bug was caused by a failure to identify LR sides of GIFTI
surfaces. SUMA was not preserving the side of a GIFTI surface
at write time in SUMA_GIFTI_Write(). Code was also modified
to guess the side of pre-existing GIFTI surfaces.
Prying was also off when a transform was found in the header
of the surface volume because dimensions were not being recomputed
after applying the VolPar transform. That is now fixed.
19 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
alignment AddEdge error
Error in resampling step of AddEdge procedure causes crash.
Problem requires both -giant_move (or -prep_off or -resample off) and
-AddEdge.
14 Mar 2013, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT)
NearestNodeCoords was added to -output_params
14 Mar 2013, ZS Saad, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT)
-init_xform now takes AUTO_CENTER_CM and CENTER_CM
14 Mar 2013, P Taylor, 3dNetCorr, level 4 (SUPER), type 1 (NEW_PROG)
New function: calculate correlat/Z of ROIs in a network.
This program works on several networks as separate subbricks simultan-
eously.
14 Mar 2013, P Taylor, rsfc, level 2 (MINOR), type 5 (MODIFY)
New functions; streamline some other functions.
For addition of 3dNetCorr, mainly.
14 Mar 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 5 (MODIFY)
List ROI labels near start of *.grid; use floor to get NmNsThr
This allows for more similarity with 3dNetCorr, and might be useful
as well if the labeling of ROIs in a network is not just 1,..,max.
The flooring vs ceiling is so that people don't have to use 0.00099
as a relative fraction of MC iterations to get the number they want.
14 Mar 2013, P Taylor, 3dDWUncert, level 2 (MINOR), type 4 (BUG_FIX)
Silly bug in e_{13}^* estimation.
Mean and std of uncertainty of e1 toward e3 was buggy.
12 Mar 2013, RW Cox, 3dNwarpApply, level 2 (MINOR), type 2 (NEW_OPT)
Various fixes
-ainterp = lets you interpolate data differently from warp
-affter = lets you use a different affine warp for each sub-brick
-nwarp = allow catenation and inversion directly on the command line
These last 2 options make the program 3dNwarpCat pleonastically
redundant.
12 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
Handling input and output directories
Output now goes to current directory (./) unless otherwise specified
with -output_dir. Thanks a lot, Rick.
11 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
Handling input and output directories
Output follows input directories unless specified with -output_dir
Previously, all input files had to exist in current directory.
Changes allow for output to follow anat or epi dataset directories
or specified output directory. Also minor change to call tcsh without
sourcing startup .cshrc
11 Mar 2013, DR Glen, @Atlasize center of mass, level 2 (MINOR), type 2 (NEW_OPT)
Add -centers for center of mass locations in atlas regions
-centers option added to @Atlasize and @MakeLabelTable
This location is simple center of mass for now and may be
outside region for non-blobbish regions
08 Mar 2013, RC Reynolds, 3dTcat, level 2 (MINOR), type 2 (NEW_OPT)
added -TR and -tpattern options
07 Mar 2013, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
handle -prefix and -overwrite for -show_bad_backslash
The combination can be used to 'fix' bad files.
27 Feb 2013, RW Cox, 3dUnifize, level 1 (MICRO), type 2 (NEW_OPT)
Added -GM option to stretch gray matter to a consistent-ish place
27 Feb 2013, RC Reynolds, python-general, level 1 (MICRO), type 2 (NEW_OPT)
added Ziad's apsearch global options: -all_opts, -h_find, -h_view
22 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Prying hemispheres apart to see medial or lateral sides simultaneously
This is controlled via the ctrl+Button 1-Motion. See SUMA's ctrl+h output
for details. The prying behaviour is different for spheres and flat maps
Just try it and see. ctrl+double click to get back to initial view.
See also env: SUMA_LHunify
22 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Automatically adjust position of LR surfaces so that they don't overlap
This is only done for anatomically incorrect surfaces, the others should
not overlap of course. This allows for simultaneous viewing of inflated
surfaces and flattened ones side by side.
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Option -anatomical labels all -i_* -t_* surfs anatomically correct
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Option -onestate put all -i_* surfs on command line in the same state
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed FOV problems for auto setting and fixing zoom level across states
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_LHunify to automatically merge LR hemispheres in all views
This is done by discarding the _lh _rh to state names that are
created by @SUMA_Make_Spec_FS
22 Feb 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 2 (NEW_OPT)
Instead of just individual ROI masks, can get map of Ntracks/voxel.
This allows a posteriori thresholding/comparisons/analysis.
22 Feb 2013, P Taylor, rsfc, level 1 (MICRO), type 4 (BUG_FIX)
Fixed potential float/double problem.
When using 3dReHo to get ReHo for ROIs, could get *very* large numbers
during part of calculations; floats were fine for 27 voxel neighborhood,
but not with large ROIs. Thus, using doubles in the calc now.
22 Feb 2013, P Taylor, 3dReHo, level 1 (MICRO), type 4 (BUG_FIX)
Fixed mask misread which could cause error in some nonmasked data.
22 Feb 2013, P Taylor, 3dDWUncert, level 1 (MICRO), type 4 (BUG_FIX)
Free as well as DELETE a dset.
Ultraminor change.
21 Feb 2013, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
small help update to include tshift block in example 5c
Thanks to J Gonzalez bringing it up.
20 Feb 2013, RW Cox, 3dUnifize, level 2 (MINOR), type 1 (NEW_PROG)
Quick and dirty approximate spatial uniformization of T1 anats
Mostly for use with 3dQwarp
19 Feb 2013, RW Cox, afni, level 2 (MINOR), type 3 (NEW_ENV)
Histogram plugins can now do cumulative distributions
set AFNI_HISTOG_CUMULATIVE to YES
15 Feb 2013, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT)
Added -FNameNoAfniExt to -out option
15 Feb 2013, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Allowed script to work with NIFTI input for both -surf_anat and -exp_anat
14 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Added stippling-based transparency to surface viewing.
Fancier blending-based transparency will have to wait.
14 Feb 2013, ZS Saad, @SUMA_Make_Spec_FS, level 3 (MAJOR), type 2 (NEW_OPT)
Option -nocor to improve data import from FreeSurfer
Option avoid COR images, produces NIFTI and GIFTI output that
aligns with the initial volume passed to FreeSurfer. This required
considerable changes to the script and will not be the default for
a while longer.
14 Feb 2013, ZS Saad, apsearch, level 2 (MINOR), type 5 (MODIFY)
Improved parsing for options to avoid getting options from sample commands
Previously, if you used an example in the help that called
a different program and you used options on clean lines as part of that
example command, those options would get attributed to the program
whose help you're reading. Pfew. Not anymore.
14 Feb 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -TransMode to control surface transparency.
14 Feb 2013, ZS Saad, @SUMA_Make_Spec_FS, level 1 (MICRO), type 2 (NEW_OPT)
Option -set_space set space of output volumes
14 Feb 2013, RW Cox, 3dAllineate, level 1 (MICRO), type 2 (NEW_OPT)
Add -emask option (exclude certain voxels)
For use in registering pre- and post-surgery volumes (e.g.).
14 Feb 2013, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
handle surface data in -move_preproc_files
Thanks to P Molfese for reporting the error.
13 Feb 2013, RC Reynolds, unix_tutorial, level 3 (MAJOR), type 1 (NEW_PROG)
added tutorial to CVS tree, with processed files under AFNI_data6
13 Feb 2013, RC Reynolds, uber_subject.py, level 1 (MICRO), type 6 (ENHANCE)
inform user of subj_dir when writing AP command
12 Feb 2013, RC Reynolds, afni_util.py, level 1 (MICRO), type 4 (BUG_FIX)
updated duplicate dataset error message to match older code updates
Thanks to HJ Jo for reporting the error.
12 Feb 2013, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX)
if 'afni -ver' fails from libraries and $status not set, check $package
11 Feb 2013, RC Reynolds, file_tool, level 1 (MICRO), type 6 (ENHANCE)
help updates
07 Feb 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Add MASK= to driver for INSTACORR INIT
Per the request of the esteemed Daniel Handwerker, scientist
extraordinaire.
07 Feb 2013, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
Added Greg Baxter's (UCSD) change for b-matrix input
06 Feb 2013, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Merged Paul Taylor's recent code changes
Also created afni_history_ptaylor.c
see afni_history -author ptaylor for details on the changes
06 Feb 2013, ZS Saad, MakeColorMap, level 2 (MINOR), type 2 (NEW_OPT)
-suma_cmap, -usercolutfile, and -sdset* options for SUMA colormaps
The new options allow users to create SUMA's colormaps with labels
and turn datasets into labeled datasets with the user's colormap
06 Feb 2013, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT)
-labelize for assigning a SUMA colormap to an integral valued dset
06 Feb 2013, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT)
Added special filename '1D:stdin' to make mri_read get 1D from stdin
In this manner, most 3d programs can now accept stdin input in 1D format
This change was suggested by Isaac Schwabacher.
06 Feb 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 2 (NEW_OPT)
Add ability to output each WM-region mask as an individual ROI.
This should make it simpler to use an ROI as a mask than
with the 2^(ROI number) labelling system within subbrick outputs.
06 Feb 2013, P Taylor, 3dTrackID, level 1 (MICRO), type 4 (BUG_FIX)
Small bug in 3dTrackID fixed.
In post-run freeing of variables, had been error for a char string.
06 Feb 2013, P Taylor, 3dRSFC, level 1 (MICRO), type 4 (BUG_FIX)
Fixed potential div by zero in 3dRSFC.
05 Feb 2013, RC Reynolds, python-general, level 1 (MICRO), type 4 (BUG_FIX)
fixed (unused) cols_by_label_list functions
Fix by I Schwabacher, who is actually using the function.
05 Feb 2013, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
updates to the help introduction
04 Feb 2013, ZS Saad, R, level 1 (MICRO), type 4 (BUG_FIX)
Properly set IDCODE of new dsets, read .1D.dset as dset not matrix
01 Feb 2013, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_ContourThickness to control the tickness of dset contour lines
Addition made in response to Valentinos' feedback.
Documentation is in .sumarc file.
31 Jan 2013, RC Reynolds, uber_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed blist error that had not been converted to bdict
Thanks to Piero C. for reporting the error.
30 Jan 2013, RC Reynolds, python-general, level 2 (MINOR), type 6 (ENHANCE)
added less biased correlations and various gcor utility functions
24 Jan 2013, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
be able to process a run of AFNI volumes (-file_type AFNI)
added for Der-Yow Chen and Cecil Yen
24 Jan 2013, RC Reynolds, 3dinfo, level 1 (MICRO), type 5 (MODIFY)
get -orient output via new THD_fill_orient_str_3
22 Jan 2013, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT)
Added -bash option for bash filename completion, & -recreate_all_afni_help
Thanks be to Isaac Schwabacher.
22 Jan 2013, ZS Saad, HalloSuma, level 2 (MINOR), type 1 (NEW_PROG)
A sample light-weight program to illustrate 2-way communication with AFNI
The program can be compiled in C or C++ along with the NIML library
without having to link to AFNI/SUMA libraries.
Documentation is the code.
22 Jan 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -echo_nel(*) option to show NIML communication elements
22 Jan 2013, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Added -hand for handeness of orientation
22 Jan 2013, ZS Saad, 3dLocalstat, level 1 (MICRO), type 5 (MODIFY)
THD_localstat() was not applying mask to output under resam. mode
22 Jan 2013, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -file_type, in prep for reading AFNI/NIfTI images
18 Jan 2013, RC Reynolds, @compute_gcor, level 2 (MINOR), type 1 (NEW_PROG)
compute GCOR = global correlation of a dataset
18 Jan 2013, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
when jobs=1, only warn for -virtvec if the option was used
The result was just a warning which did not affect processing.
Thanks to J Britton and E Ronkin for reporting the warning.
16 Jan 2013, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -dc_params
To go with new scripts AFNI_data6/realtime.demos/demo.2.fback.*.
16 Jan 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -show_gcor (and _all and _doc)
compute GCOR (average correlation) on 1D files
11 Jan 2013, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT)
Added -flip_orient option to change orientation of triangles.
09 Jan 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -regress_compute_gcor
If errts and EPI mask exist, GCOR is computed by default.
07 Jan 2013, ZS Saad, 3dinfill, level 2 (MINOR), type 2 (NEW_OPT)
Added -radial_* options to test SUMA_Volume_RadFill() function.
07 Jan 2013, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
added option -l2norm, to compute L2 norm
04 Jan 2013, DR Glen, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug that would make 3drefit exit if dataset contains a warpdrive attribute
02 Jan 2013, RW Cox, afni Clusterize, level 2 (MINOR), type 5 (MODIFY)
Allow use of Spearman rather than Pearson for scatterplot correlation
Set via environment variable AFNI_CLUSTER_SPEARMAN, or by popup menu
attached to top of clusterize report form. This is for PK.
02 Jan 2013, RC Reynolds, 3dCM, level 1 (MICRO), type 4 (BUG_FIX)
in THD_cmass(), if mask is NOT set, clear data value
Found with dglen. This is an old bug, ick.
31 Dec 2012, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
is_in_labels(): search for longest match
To fix failure in the case of both label and labelSUFFIX existing.
28 Dec 2012, RC Reynolds, suma-general, level 1 (MICRO), type 4 (BUG_FIX)
mri_polyfit() now takes exar paramter, pass NULL
27 Dec 2012, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Increased buffer size for reading one line.
See LBUF in mri_read.c, also added error message when
line is too long for LBUF in afni_fgets()
27 Dec 2012, RW Cox, 3dPolyfit, level 1 (MICRO), type 2 (NEW_OPT)
Add '-base' option
To allow fitting (in space) arbitrary input images, as well as (spatial)
polynomials.
26 Dec 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT)
-virtvec option for Javier
21 Dec 2012, ZS Saad, @clip_volume, level 1 (MICRO), type 2 (NEW_OPT)
Added options -crop_allzero and -crop_greedy.
21 Dec 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX)
change check for recur download by looking for known string in script
Thanks to S Lowell for reporting the error.
20 Dec 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 4 (BUG_FIX)
remove -volreg_tlrc_warp in case of no tlrc block
Thanks to P Taylor for reporting the error.
19 Dec 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 0 (GENERAL)
Update from Rayus for handling .nii files.
18 Dec 2012, ZS Saad, cat_matvec, level 1 (MICRO), type 2 (NEW_OPT)
option -4x4 to output augmented matrix.
18 Dec 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
have THD_subbrick_minmax fall back to THD_slow_minmax_dset if no STAT
This is a fix for 3dSkullStrip on NIfTI dsets.
Thanks to kelvin for reporting the error.
05 Dec 2012, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
add Detrend button to Opt menu
Detrends each time series before plotting. For Javier.
05 Dec 2012, RC Reynolds, serial_helper, level 1 (MICRO), type 0 (GENERAL)
added useless string specifier in snprintf to block compier warnings
Requested by Y Halchenko.
03 Dec 2012, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY)
Added temporary overwriting without upsetting initial setting
See THD_get_ok_overwrite()
03 Dec 2012, ZS Saad, 3dSkullStrip, level 1 (MICRO), type 5 (MODIFY)
More modifications for head extraction
Approach now uses 'Radial Stats' for head/non-head separation.
See functions SUMA_THD_Radial_HeadBoundary(), SUMA_ShrinkSkullHull_RS()
and SUMA_ExtractHead_RS()
29 Nov 2012, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
add -f to 'tcsh -c' for getting output from commands
Thanks to P Molfese for the suggestion to avoid .cshrc text output.
28 Nov 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
-dospcov
Compute Spearman correlation of subject results with covariate. Output
sub-bricks are labeled with '_SP' at the end, as in 'LLL_cov_SP' to
indicate the group with label 'LLL' correlated with the covariate with
label 'cov'. This is for the IMom (PK).
26 Nov 2012, RC Reynolds, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
added -save_script option
added script history in afni_com class
23 Nov 2012, RW Cox, afni instacorr, level 2 (MINOR), type 5 (MODIFY)
Allow Start and End indexes, rather than Ignore (=Start)
To allow Instacorr-ing a subset of a time series. Per the request of
the Exceptional Javier Gonzalez-Castillo
15 Nov 2012, ZS Saad, AFNIio.R, level 2 (MINOR), type 5 (MODIFY)
Made read.AFNI and write.AFNI more clever
Changes included: AUTO method selection, dset.attr() improvements
to handle dset structures or their headers from either clib or Rlib
functions. Micro change to THD_dblkatr_from_niml which crashed for
null strings.
15 Nov 2012, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Guarded against NULL strings in THD_dblkatr_from_niml()
These strings came via R_io.c, but could come from elsewhere.
15 Nov 2012, RC Reynolds, 3dTqual, level 2 (MINOR), type 2 (NEW_OPT)
added -mask option
Requested by evangelou.
14 Nov 2012, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed check for random space in -max_consec case
Thanks to Kristina for reporting the error.
13 Nov 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fixed fopen_maybe to check for .1D suffix on file streams
Suffix might get added by EDIT_dset_items.
Thanks to I Schwabacher for reporting the error.
12 Nov 2012, ZS Saad, @T1scale, level 2 (MINOR), type 2 (NEW_OPT)
Straight and weighted divisions of T1 by PD, and initial alignment
The weighted volume allows one to keep the high-res. aspect of
PD division, while considerably reducing the extreme enhancement.
12 Nov 2012, ZS Saad, 3dHist, level 2 (MINOR), type 2 (NEW_OPT)
Added -cmask and -quiet to 3dHist
09 Nov 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash on OSX 10.7_64 apparently caused by gcc's optimization
The fix entailed adding -O1 to target SUMA_xColBar.o in SUMA's
SUMA_Makefile_NoDev. I also changed the way SurfaceControllers
are put away. They are now minimized thus keeping the widgets
realized.
06 Nov 2012, ZS Saad, 3dkmeans, level 2 (MINOR), type 2 (NEW_OPT)
Added -write_dists to only output ascii files when users want them
The changes were made to also cleanup the output of 3dSeg.
06 Nov 2012, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 2 (NEW_OPT)
Added -head*, and -cut_below options to generate whole head masks
This was needed because 3dAutomask or 3dSkullStrip would fail atcreating w
hole head masks for cases with coil-array shading problems
and/or lots of noise.
01 Nov 2012, ZS Saad, suma-general, level 1 (MICRO), type 3 (NEW_ENV)
Abide by AFNI's AFNI_FLOATSCAN variable and look for bad values
SUMA will now scan for bad floats (NAN, and INF) and sets them
to 0, when the dataset is loaded. You can turn this feature off
with AFNI_FLOATSCAN set to NO.
01 Nov 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed problem with very large threshold ranges
X11 scale cannot range more than MAX_INT/2. SUMA nowchecks for that and wa
rns the user.
23 Oct 2012, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
forgot to leave show_size_n_offset set
Thanks to J Jarcho for reporting the to3d failure.
19 Oct 2012, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
added test for BOM bytes (byte order mark)
19 Oct 2012, G Chen, 3dMVM, level 3 (MAJOR), type 1 (NEW_PROG)
Multivariate modeling approach to group analysis
This is an R program that performs conventional ANOVA or
ANCOVA-type analysis with no limit on the number of variables.
See more details at http://afni.nimh.nih.gov/sscc/gangc/MVM.html
18 Oct 2012, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_CREEPTO modifies 'jumpto xyz' behavior
18 Oct 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 4 (BUG_FIX)
small updates to correspond with library changes
18 Oct 2012, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
added convenience option -test
17 Oct 2012, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Add 'j' and 'f' keystrokes for image viewers
Like 'Jump' and 'Flash' in the Clusterize Rpt windows, for the cluster
in which the crosshairs currently reside.
17 Oct 2012, RC Reynolds, dicom_hdr, level 2 (MINOR), type 2 (NEW_OPT)
added -no_length option, which helps when running diffs on output
17 Oct 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
removed unneeded -set_tr from 1d_tool.py -censor_motion
16 Oct 2012, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed functions that generate volume masks from surfaces
There was a bug in SUMA_FindVoxelsInSurface() and SUMA_SurfGridIntersect()
which made for ugly masks in the fast mode. This is no longer the case,
SUMA_FindVoxelsInSurface() is about as good as its sister function
SUMA_FindVoxelsInSurface_SLOW(), but considerably faster.
This bug fix might affect some 3dSkullStrip and 3dSurfMask results. The
more voxel sizes differ from 1x1x1, the more noticeable the difference
might be.
16 Oct 2012, ZS Saad, 3dSurfMask, level 1 (MICRO), type 2 (NEW_OPT)
Option -no_dist to avoid length distance computations.
Also, the fast method was improved per the comment below.
16 Oct 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT)
added analysis type and processing block list
16 Oct 2012, DR Glen, afni show atlas colors, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug that would crash afni if paned color and show atlas colors
15 Oct 2012, ZS Saad, @T1scale, level 2 (MINOR), type 2 (NEW_OPT)
A better masking option using -brainhull
The option seems pretty good at creating brain mask from pretty
lousy data.
15 Oct 2012, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Add 'range=a,b' option to ALTER_WINDOW command in AFNI driver
15 Oct 2012, RW Cox, 1dplot, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug with -CENSORTR run wildcards and coloring
15 Oct 2012, RW Cox, 1dplot, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug with 'push' and '-yaxis' interacting badly.
13 Oct 2012, ZS Saad, 3dHist, level 2 (MINOR), type 1 (NEW_PROG)
Computes histograms using functions from the segmentation routines
The program uses heuristics to automatically select histogram
parameters, and it allows histogram queries.
It had to be separate from 3dhistog because it uses libSUMA.a and because
the latter's interface was getting too complicated.
13 Oct 2012, ZS Saad, 3dinfo, level 1 (MICRO), type 2 (NEW_OPT)
-voxvol returns a voxel's volume in mm cubed
12 Oct 2012, ZS Saad, 3dedge3, level 2 (MINOR), type 4 (BUG_FIX)
Fixed scaling problem for short/byte data.
12 Oct 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
added byte-swapping for complex numbers in thd_niml.c
12 Oct 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
included tshift block in example #9 - resting state analysis
Thanks to D Drake for reminding me to add it.
12 Oct 2012, RC Reynolds, @RetinoProc, level 1 (MICRO), type 4 (BUG_FIX)
set AEA_opt in quotes, as it might be a list
10 Oct 2012, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT)
Added yoking of 1_only, Dim, and Opacity controls
10 Oct 2012, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT)
Added -Opa to control opacity
10 Oct 2012, ZS Saad, @RetinoProc, level 1 (MICRO), type 2 (NEW_OPT)
Option -AEA_opts for passing arguments to align_epi_anat.py
09 Oct 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Allow input of surface-based complex time series.
SUMA will report and graph the magnitude of complex data
Other transformations can be added when needed.
Surface data I/O were modified to allow handling
of complex-typed data including functions in thd_niml.c, and thd_gifti.c
Programs like 3dDFT and 3dcalc can read/write complex surface-
based datasets.
09 Oct 2012, ZS Saad, 3dDFT, level 2 (MINOR), type 2 (NEW_OPT)
Allow handling of complex surface-based data
Earlier versions could not output complex data for surface-based datasets.
Minor changes to the help output to fix order of -cx2r option and
allow option suggesting.
09 Oct 2012, ZS Saad, 3dttest++, level 1 (MICRO), type 5 (MODIFY)
Micro modification of verbose output to flag paired from unpaired tests
09 Oct 2012, ZS Saad, 3dcalc, level 1 (MICRO), type 5 (MODIFY)
Clarify help for -cx2r, and allowing -help in mid command.
05 Oct 2012, RC Reynolds, dicom_hinfo, level 2 (MINOR), type 2 (NEW_OPT)
added option -no_name
05 Oct 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -quick_censor_count
04 Oct 2012, ZS Saad, afni-matlab, level 2 (MINOR), type 2 (NEW_OPT)
Minor tweaks to WriteBrik and BrikInfo
WriteBrik can automatically set some header fields (AdjustHeader option)
BrikInfo now loads IJK_TO_DICOM_REAL
04 Oct 2012, ZS Saad, MapIcosahedron, level 1 (MICRO), type 4 (BUG_FIX)
Dset Mapping failed on sparse datasets, at times.
04 Oct 2012, ZS Saad, 3dedge3, level 1 (MICRO), type 5 (MODIFY)
Updated 3DEdge library to GPL version: 2012-02-22
03 Oct 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
dashed parameters are now illegal for many options in many python programs
Affects programs:
1d_tool.py, afni_proc.py, gen_group_command.py, make_random_timing.py,
make_stim_times.py, option_list.py, timing_tool.py
02 Oct 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
added stim_type column to stim table
This corresponds to the afni_proc.py option -regress_stim_types.
02 Oct 2012, RC Reynolds, model_conv_diffgamma, level 1 (MICRO), type 0 (GENERAL)
small help update
01 Oct 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added 'file' to list of -stim_types parameters
The 'file' type would imply -stim_file in 3dDeconvolve, not timing.
28 Sep 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG)
Added Paul Taylor's map_TrackID to warp tracks by an affine transform
28 Sep 2012, ZS Saad, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT)
Enabled automatic centering via -init_xform
You can use -init_xform AUTO_CENTER or -init_xform CENTER
to perform center alignment during registration.
28 Sep 2012, ZS Saad, @T1scale, level 2 (MINOR), type 1 (NEW_PROG)
A mini script to scale T1s by PD volumes
Script uses method borrowed from @CalculateSignatures
to reduce bias field in T1 using a PD volume. Script also
works well without PD.
28 Sep 2012, ZS Saad, 3dTrackID, level 1 (MICRO), type 2 (NEW_OPT)
Option -rec_orig to record dataset origin in tractography output
26 Sep 2012, RC Reynolds, nifti_tool, level 2 (MINOR), type 4 (BUG_FIX)
changed ana originator field from char to short
26 Sep 2012, RC Reynolds, @update_afni_binaries, level 2 (MINOR), type 2 (NEW_OPT)
added -apsearch; verify download for recursive step
25 Sep 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
use errts_REML to compute blur if 3dD_stop; apply compute_fitts if no reml
Thanks to P Molfese for reporting the problem.
22 Sep 2012, ZS Saad, @SUMA_Make_Spec_Caret, level 1 (MICRO), type 5 (MODIFY)
Updated script to work with current Caret release
22 Sep 2012, ZS Saad, 3dkmeans, level 1 (MICRO), type 4 (BUG_FIX)
Fixed default prefix which was overwriting input.
Also added default selection when input has single value
21 Sep 2012, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY)
pkundu update
21 Sep 2012, RC Reynolds, 3dNLfim, level 1 (MICRO), type 0 (GENERAL)
added ConvDiffGam to help
20 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
added some projection function to python libraries
20 Sep 2012, RC Reynolds, 3dClustSim, level 1 (MICRO), type 0 (GENERAL)
added a note to the help about computing blur estimates
Requested by J Weisberg.
19 Sep 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add -scale option for the Person from Kolkata
18 Sep 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG)
Checked in Prantik Kundu's MEICA tools.
Try meica.py -help, also try @Install_MEICA_Demo
13 Sep 2012, ZS Saad, 3dhistog, level 2 (MINOR), type 2 (NEW_OPT)
Added -pdf to 3dhistog to make area = 1
13 Sep 2012, RC Reynolds, afni_util, level 2 (MINOR), type 6 (ENHANCE)
can call list functions via -listfunc (to avoid input formatting)
Also, use -join after the LISTFUNC to remove list format on output, e.g.
cd AFNI_data6
afni_util.py -listfunc list_minus_glob_form -join group_results/OLSQ*.HEAD
13 Sep 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
download and run the current version on the web site
Good idea, Bob.
12 Sep 2012, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Stupid null character termination missing in THD_filepath()
12 Sep 2012, ZS Saad, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
Fixed incorrect warning in 3dttest++ about labels and filenames
The warning is intented to be sure users don't mess up the
-setA option when using the long form. The warning message
was being triggered incorrectly, this should no longer be the case.
Warning did not affect results.
11 Sep 2012, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Began merger of surface controllers
The idea is to have all surface controllers in one window
in order to save on screen space. Looks promising but must be
rolled out carefully because surface controllers permeate everything.Use e
nvironment variable SUMA_SameSurfCont to turn feature on.
Make sure it is debugged with valgrind too.
11 Sep 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed 'potential' crash in SUMA_SetScaleThr_one()
11 Sep 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed potential corruption in macro SUMA_NEL_REPLACE_STRING
Not sure to make of this problem, but bad reads/writes
are happening in m_rc[(row)] in the macro, and to cs[n0++]
in cs[n0++] = lbl[i]; of SUMA_AddColAtt_CompString(). In fact
the first problem happens in cs[n0++], so the problem might
start there. In any case, the fix was to increase the length
of allocated segment by +10 instead of +1 in SUMA_NEL_REPLACE_STRING
That seems to do the trick.
10 Sep 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Typing in sub-brick arrow fields was ignored on linux
Problem due to incorrect error checking from strtod()
07 Sep 2012, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT)
SUMA now highlights cluster |max|, rather than max
06 Sep 2012, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT)
Added -no_volreg for time series already registered
06 Sep 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
SUMA's sub-brick arrowfields were not updating properly
06 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
if varying facs/types on NIfTI write, write floats instead of failing
06 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
apply global opt -pad_to_node when going through AFNI format in thd_niml.c
06 Sep 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY)
print missing xmat error w/out debug, as it is fatal
05 Sep 2012, ZS Saad, @CalculateSignatures, level 2 (MINOR), type 2 (NEW_OPT)
Added possiblity to scale by top percentiles with -FATscl
This would produce .sc9 outputs. It looks like the scaling is
more promising than by MEDIAN(20) or MAD(20).
05 Sep 2012, ZS Saad, 1dRplot, level 2 (MINOR), type 2 (NEW_OPT)
Made program take in histograms produced by 3dGenFeatureDist
This required changes to AFNIio.R so that NIML groups are not
automatically sent to the distbin. Instead, the first element
in the ni_group is returned.
05 Sep 2012, ZS Saad, 3dGenFeatureDist, level 1 (MICRO), type 2 (NEW_OPT)
Program now creates the feature correlation matrix per class.
Both histograms and correlation matrices are stored in NIML
format under a directory named by the user.
04 Sep 2012, ZS Saad, 3ddot, level 2 (MINOR), type 2 (NEW_OPT)
Made program output niml 1D format, makes it easy to plot with 1dRplot
04 Sep 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -regress_ROI
This allows for tissue-based regression, with ROI averages from any of:
brain (from full_mask), GM, WM and CSF (from Classes_resam)
The 'mask' block is required for all ROIs, and option -mask_segment_anat
is required for the latter 3.
04 Sep 2012, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed error message in case of different group sizes
Error pointed out by Priyank.
31 Aug 2012, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
added option -signed_absmax
Requested by P Hamilton.
30 Aug 2012, ZS Saad, 3ddot, level 2 (MINOR), type 2 (NEW_OPT)
Made program create corr. matrix as opposed to just one pair of sub-bricks
Output is also beautified with option -show_labels
30 Aug 2012, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 5 (MODIFY)
display -show_mmms output to 4 places
29 Aug 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Allowing yoking of intensity to node selection.
Ctrl+Button-3 would select a node and switch intensity sub-brick
to that node's index * K. This is only done if the dataset currently
viewed has as K times as many sub-bricks as the surface has nodes.
K being an integer, naturally.
Nick Oosterhoff instigated this business
29 Aug 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
AFNI build was failing on machines where DONT_USE_MCW_MALLOC was defined
The cause of failure was a missing #define NI_calloc() when
DONT_USE_MCW_MALLOC is defined. The one line needed is now in niml.h.
Builds likely affected are solaris and macosx_10.7_Intel_64
Affected build dates from about Aug. 24th to Aug. 29th.
28 Aug 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed interaction with L/R yoking asynchrony.
Problems included interaction with clustering setting and with
Intensity/Threshold/Brightness selectors.
28 Aug 2012, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT)
Preserved controller settings for newly loaded or reloaded dsets
The preserved settings include clustering options.
28 Aug 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed some L/R yoking problems and a crash source in drive mode.
The crash was caused when calling SUMA_Set_Menu_Widget() on a controller
not fully realized.
27 Aug 2012, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY)
Modifed THD_load_tcat() to include subbrick labels in auto catenation
Also, started checking for datatype mixing and issuing warning when needed
.
24 Aug 2012, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Added interactive clustering to surface controller
The state of affairs:
-Clustering tables are only output to the terminal
and the log window.
-Clustering is yoked between hemispheres
-Can control connectivity radius and min area or min nodes
-When you click on a node inside a cluster, the node in that
cluster with the highest value is highlighted with a black
sphere.
24 Aug 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG)
Added Paul Taylor's 3dRSFC to the distribution
24 Aug 2012, ZS Saad, @CalculateSignatures, level 2 (MINOR), type 2 (NEW_OPT)
Added coordinate feature generation, if TLRC xform is provided
Note that the TLRC xform need not be too precise. The coordinate
features are not intended to make sure of segmentation templates.
24 Aug 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed SUMA<-->AFNI cross hair linkage with multiple anat. correct surfaces
It used to be that a coordinate always got attached to the Local Domain
Parent surface. Even if you clicked closest to a node on the Pial surface
SUMA would jump to the correspoding node on the smoothwm surface. This was
way uncool.
24 Aug 2012, ZS Saad, niprobe, level 1 (MICRO), type 1 (NEW_PROG)
A variant on niccc to handle certain NIML file probing operations
24 Aug 2012, ZS Saad, SurfClust, level 1 (MICRO), type 2 (NEW_OPT)
Allow -i* form of surface input
24 Aug 2012, ZS Saad, @ScaleVolume, level 1 (MICRO), type 4 (BUG_FIX)
step(a) was used instead of bool(a) for masking operations
This caused zeros in the output where input values were negative.
Also added a modifier to the labels to highlight that features were
scaled.
24 Aug 2012, ZS Saad, @SUMA_Make_Spec_FS, level 1 (MICRO), type 5 (MODIFY)
Made script port more datasets from FreeSurfer (depth, curvature)
24 Aug 2012, RC Reynolds, column_cat, level 3 (MAJOR), type 1 (NEW_PROG)
like 'cat', except horizontally (see recent Unix command, 'paste')
23 Aug 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT)
can pass -censor_dset
21 Aug 2012, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 2 (NEW_OPT)
added 'sigma' uvar, for passing to SurfSmooth
20 Aug 2012, ZS Saad, SurfExtrema, level 1 (MICRO), type 2 (NEW_OPT)
Made default input the convexity of the surface
17 Aug 2012, RC Reynolds, 3dGroupInCorr, level 1 (MICRO), type 4 (BUG_FIX)
pass 'batch mode' var to SUMA_init_GISET_setup to preserve dset
16 Aug 2012, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 5 (MODIFY)
show datasets names when a 'labels not unique' error occurs
15 Aug 2012, ZS Saad, 3drefit, level 2 (MINOR), type 2 (NEW_OPT)
Added -sublabel_prefix and -sublabel_suffix
15 Aug 2012, DR Glen, whereami web, level 1 (MICRO), type 4 (BUG_FIX)
Web-based atlases would not open webpage with ampersands, punctuation
14 Aug 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
match default class order for 3dSeg; copy labeltable into resampled dset
14 Aug 2012, DR Glen, whereami minimum probability, level 2 (MINOR), type 2 (NEW_OPT)
Minimum probability option to consider for probabilistic atlases
Can set option, -min_prob, or environment variable,
AFNI_WHEREAMI_PROB_MIN, to control output of whereami reports or
masks from probabilistic atlases
14 Aug 2012, DR Glen, 3drefit -epan error, level 2 (MINOR), type 4 (BUG_FIX)
Removed error for refitting data type
3drefit would exit with error for -epan and multi-subbrick data
Removed incorrect checks against archaic timepoints per TR nvals
10 Aug 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 0 (GENERAL)
Updates from Rayus.
Fixed bugs with -outcensor and -snr.
Added -bpassregs and -keepuncensored.
Use variable detrending for -tsnr.
09 Aug 2012, RC Reynolds, afni_general, level 1 (MICRO), type 4 (BUG_FIX)
definition after ENTRY in mri_genalign_util.c
08 Aug 2012, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Improved handling of coords in 'cm' units and better axis text layout
Surfaces with coords in cm were poorly displayed and without warning.
Now you are urged to make use of the SUMA_NodeCoordsUnits env .
Axis text labels were also improved to reduce clobbering.
08 Aug 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -use_slice_loc; fixed app of use_last_elem in mri_read_dicom
g_info.use_last_elem has usurped the lone global
08 Aug 2012, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 4 (BUG_FIX)
currently need to pass -sv even for -on_surface; get rid of this later
08 Aug 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
do not update tlrc anat with strip if passed in
06 Aug 2012, DR Glen, NIFTI reading, level 2 (MINOR), type 3 (NEW_ENV)
Handling view equivalents for NIFTI
AFNI_NIFTI_VIEW sets default view for AFNI datasets marked as
'aligned' (sform_code or qform_code = 2). This variable should
be set to 'TLRC', 'ORIG' or 'ACPC'.
03 Aug 2012, RW Cox, 2perm, level 1 (MICRO), type 1 (NEW_PROG)
For generating 2 random subsets of a sequence of integers
31 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
have -mask_segment_anat default to no (libgsl is not quite so common)
31 Jul 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
speed up reading NIfTI files with long histories (THD_dblkatr_from_niml)
Thanks to J Gonzalez for reporting the problem.
31 Jul 2012, RC Reynolds, 3dresample, level 2 (MINOR), type 4 (BUG_FIX)
update IJK_TO_DICOM and _REAL at end of resample library function
Thanks to I Schwabacher for reporting the IJK_TO_DICOM discrepancy.
30 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
if surface analysis, create run_suma script
30 Jul 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_mmms
Display min, mean, max, stdev of each column.
26 Jul 2012, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
Modify wsinc5 (again) to be more flexible
26 Jul 2012, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_comm_times option to show communication times
Added for J Evans (and to get it off an ancient todo list).
26 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -mask_segment_anat and -mask_rm_segsy
If anat is stripped, create segmented anat unless user says not to.
26 Jul 2012, RC Reynolds, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
K text columns (after label) would result in K lost float columns
Thanks to Phoebe of Harvard for reporting the problem.
23 Jul 2012, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
Also, change wsinc5 taper from Hanning to Hamming
23 Jul 2012, RW Cox, 3dAllineate, level 1 (MICRO), type 3 (NEW_ENV)
Allow 7x7x7 interpolation in wsinc5 + spherical mask
via environment variables
23 Jul 2012, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
allow programs to read auto-tcat datasets using filelist:DSETS.txt
If DSETS.txt contains a list of datasets, they will be read in using
THD_open_tcat(), as if they were listed separated by spaces.
Added for C Connolly.
20 Jul 2012, RC Reynolds, apsearch, level 1 (MICRO), type 5 (MODIFY)
exclude README.* from program list
Executable README files can be troublesome...
19 Jul 2012, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Allow for L/R hemi yoking for many operations
These include:Threshold setting. I,T,B sub-brick selection. Range
setting. Dset loading. Cmap changing. Dset switching.
Order changing.
19 Jul 2012, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
New variables to initialize range setting and symmetric range
See SUMA_Auto_I_Range, SUMA_Auto_B_Range, and SUMA_Sym_I_Range
in ~/.sumarc . If you don't see them, time to run: suma -update_env
18 Jul 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG)
Added Paul Taylor's 3dReHo to the distribution
17 Jul 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY)
added checks for volreg and uncensored X-mat; get view from volreg
17 Jul 2012, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 5 (MODIFY)
removed -Niter opt from SurfSmooth (let it decide)
12 Jul 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT)
added ':a:b:c' appendage to -stim_times_AM2
To allow user to specify what values to subtract from modulation
parameters (over-riding the default subtraction of the average).
11 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
fill gaps and holes in anatomical masks
(now requires AFNI from 7 May, 2012)
10 Jul 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Made default prefix path be ./ instead of path of input
The change was done to function EDIT_empty_copy() which assigned
to a pathless prefix the path of the input dataset if the latter
was specified. The problem was that something like:
3dMean -prefix mmm P1/joe+orig P2/jane+orig
would have written mmm+orig under P1/
To make matters less palatable other programs like 3dcalc behaved
differently: 3dcalc -prefix ccc -a P1/joe+orig -expr 'a'
would produce ./ccc+orig
10 Jul 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
let the user know whether 3dClustSim will be run
09 Jul 2012, RC Reynolds, align_epi_anat.py, level 1 (MICRO), type 5 (MODIFY)
escape (unalias) every 'rm' command
09 Jul 2012, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 5 (MODIFY)
escape (unalias) every 'rm' command
06 Jul 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Use ArrowFields when datasets have large numbers of sub-bricks
The switch is done automatically and is controlled with env:
SUMA_ArrowFieldSelectorTrigger
06 Jul 2012, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ArrowFieldSelectorTrigger set threshold for using ArrowFields
For datasets with sub-bricks >= SUMA_ArrowFieldSelectorTrigger
and arrow field is used to switch between sub-bricks
29 Jun 2012, RC Reynolds, @Install_RSFMRI_Motion_Group_Demo, level 2 (MINOR), type 1 (NEW_PROG)
program is for installing demo of RSFMR on big and small motion groups
29 Jun 2012, RC Reynolds, prompt_user, level 1 (MICRO), type 2 (NEW_OPT)
if MESSAGE is '-', read from stdin
29 Jun 2012, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY)
moved ptaylor_install dependency from 'vastness' to 'install'
28 Jun 2012, ZS Saad, ROIgrow, level 2 (MINOR), type 2 (NEW_OPT)
Added -insphere and -inbox options
These options grow ROIs by finding nodes that fall inside a box or sphere
of preset size around nodes in the original ROIs.
28 Jun 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed help error regarding IM
Thanks to I Blair for reporting it.
28 Jun 2012, DR Glen, Draw Dataset plugin, level 2 (MINOR), type 4 (BUG_FIX)
Resampling of atlas regions to lower resolution undercounted
Draw Dataset plugin atlas resampling to a lower resolution dataset
undercounts number of voxels. Incorrect usage of temporary volume
in byte storage was fixed with float volume. Additionally, new
environment variable, AFNI_DRAW_THRESH, allows for variable
threshold level (done with RCR)
27 Jun 2012, RC Reynolds, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT)
added -nzmedian, requested on message board
25 Jun 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed uninitialized cpad1,2 in the case of no censoring
25 Jun 2012, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 6 (ENHANCE)
added help for -factors and 3dANOVA3 -type 4 examples
22 Jun 2012, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT)
added commands 3dANOVA2 and 3dANOVA3; added option -factors
Need to add help for -factors (i.e. for 3dANOVA3 -type 4).
20 Jun 2012, RC Reynolds, plug_realtime, level 1 (MICRO), type 4 (BUG_FIX)
comment out plot_ts_setthik() type calls for now
When registering, finalize_dset() will result in white image window.
Thanks to V Roopchansingh for reporting the problem.
19 Jun 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Ctrl+W was not saving datasets when filenames contained a path
Problem had to do with clumsy prefix forming.
19 Jun 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -switch_cmode to allow switching how values map to colors
This controls the 'Col' menu in SUMA's surface controller.
19 Jun 2012, RW Cox, 3dttest++, level 2 (MINOR), type 0 (GENERAL)
Internal wildcard expansion with SHORT FORM '-set' options.
15 Jun 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_censor_extern
15 Jun 2012, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
make num_dim violation a warning, because of mris_convert
14 Jun 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
use afni -com instead of plugout_drive (for case of multiple users)
Thanks to V Razdan and N Adleman for reporting the issue.
06 Jun 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
look for input of EPI datasets in standard space and NIfTI format
05 Jun 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
warn users if married types and files do not seem to match
05 Jun 2012, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 4 (BUG_FIX)
need to explicitly set DSET_BRICK_TYPE() on some systems
04 Jun 2012, ZS Saad, @Install_TSrestMovieDemo, level 1 (MICRO), type 1 (NEW_PROG)
Demo script to make a resting state movie a la Daniel Margulies'
04 Jun 2012, ZS Saad, @Install_AfniRetinoDemo, level 1 (MICRO), type 1 (NEW_PROG)
Demo script to download and run Retinotopy pipeline demo
03 Jun 2012, RC Reynolds, uber_subject.py, level 1 (MICRO), type 6 (ENHANCE)
for variable updates: actually show list if it is short enough
03 Jun 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
for resting state analysis, suggest -regress_censor_motion 0.2
Suggest a more strict limit for resting state than for task analysis.
01 Jun 2012, ZS Saad, 3dROIstats, level 1 (MICRO), type 4 (BUG_FIX)
3dROIstats crashed on float dsets with scaling. Not anymore
Problem was scaling brick pointer without mallocizing first.
31 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Merged ptaylor's code changes into the distribution
auto-generated by afni_history on May 30 2013