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 2
---- log of AFNI updates (most recent first) ----
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
30 May 2012, DR Glen, 3dinfo, 3drefit, level 2 (MINOR), type 5 (MODIFY)
av_space option handling and orig/other space refitting
3dinfo reports view extension for -av_space instead of generic
space view extension. 3drefit will warn if setting non-orig
space on orig view data or orig space on tlrc view data.
25 May 2012, ZS Saad, SurfToSurf, level 1 (MICRO), type 4 (BUG_FIX)
Improve auto-name generation and enabled output format specification
25 May 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
display modified options and subject defaults
24 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Merger of changes in P. Taylor's code
24 May 2012, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
csf_val and csf_fa options apply to linear solutions too
23 May 2012, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT)
Allow label-based selection for annotation files
See function: process_NSD_labeltable(), now you can do something like:
3dcalc -a std.60.lh.aparc.a2009s.annot.niml.dset'' \
-expr 'step(a)' -prefix wm_lh_G_precentral.niml.dset
23 May 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add -clust option, to allow 3dClustSim stuff to be used
23 May 2012, DR Glen, 3dinfo, @auto_tlrc, level 3 (MAJOR), type 4 (BUG_FIX)
Generic space handling corrected for TT_N27 and other spaces
@auto_tlrc would crash with improper generic spaces
Generic space restricted to AFNI view names (orig, acpc, tlrc)
22 May 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT)
added regress_bandpass and regress_mot_deriv (probably for resting state)
22 May 2012, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
csf_val and csf_fa options for default values if B=0 less than gradient values
21 May 2012, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT)
Made program output mapping info file for use with SurfToSurf
Also made microscopic improvement to automatic dset name generation for -d
set_map
21 May 2012, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Made the script also port thickness data and take them to std. space
21 May 2012, ZS Saad, 3dTcorrelate, level 2 (MINOR), type 2 (NEW_OPT)
Added -covariance option, turned off DOF setting for anything but pearson.
See function THD_covariance()
21 May 2012, ZS Saad, SurfToSurf, level 1 (MICRO), type 4 (BUG_FIX)
Microscopic improvement to automatic dset name generation for output dsets
21 May 2012, ZS Saad, ROIgrow, level 1 (MICRO), type 4 (BUG_FIX)
ROIgrow was not taking -spec surface definition
21 May 2012, RW Cox, FDR calculations, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_NON_INDEPENDENT_FDR == YES --> like '-cdep' in 3dFDR.
21 May 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added the long-desired-but-not-so-needed -regress_stim_types option
This allows users to specify -stim_times/_AM1/_AM2/_IM.
19 May 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
added help examples for resting state analysis
19 May 2012, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
allow for auto-tcat of 1D inputs that are separated by spaces
For E Demir to use in 3dDeconovolve.
17 May 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add -donocov option
When -covariates is used, -donocov says to also do the NO covariates
analyses and tack them onto the end of the results -- for comparison fun
16 May 2012, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 5 (MODIFY)
do not ask for user input, even if centers are off by 80+ mm
16 May 2012, RC Reynolds, @GetAfniOrient, level 1 (MICRO), type 5 (MODIFY)
suppress 3dinfo version text
15 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
Added '[1dcat FF.1D]' syntax for sub-brick selections in 1D file
This was added for the same reason '[count ...]' was added, and
that is to allow for lengthy selection values. Dealing with selections
of 100+ sub-bricks virtually guarantees some string limit is reached,
somewhere. See 3dTcat -help for details
15 May 2012, ZS Saad, 1dRplot, level 1 (MICRO), type 2 (NEW_OPT)
Added -load.Rdat to regenerate previous plot on command line
11 May 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
also output average censored per-TR motion
10 May 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
allow for a wider range of file names
- handle case of more than 99 runs
- look for files of the form *_rall.1D, as well as *.rall.1D
10 May 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow processing of more than 99 runs
08 May 2012, ZS Saad, count, level 2 (MINOR), type 2 (NEW_OPT)
Added -form to count: count -form %c 49 130
08 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Code updates for P. Taylor's tractography
08 May 2012, ZS Saad, 3dSeg, level 2 (MINOR), type 4 (BUG_FIX)
Fixed memory leak problem
08 May 2012, RW Cox, 1ddot, level 1 (MICRO), type 2 (NEW_OPT)
Add -rank option to do Spearman correlations
08 May 2012, DR Glen, 3dinfo, level 1 (MICRO), type 2 (NEW_OPT)
gen_space option to see generic space type for a dataset
07 May 2012, RW Cox, FIRdesign, level 1 (MICRO), type 1 (NEW_PROG)
Finite Impulse Design filter design program -- for bandpass
07 May 2012, RW Cox, AFNI instacorr, level 1 (MICRO), type 5 (MODIFY)
Modify treatment of Global Ort file
If too short to allow for Ignore, then doesn't do Ignore on the Global
Ort time series. Otherwise, does the initial Ignore on that input. The
Help also reflects this change. In the past, it always did the Ignore
on the Global Ort data, and if it couldn't, then it skipped them
entirely.
07 May 2012, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 6 (ENHANCE)
replaced THD_mask_erode with new THD_mask_erode_sym
This change should make dilate and erosion operations symmetric.
07 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added weighted_enorm method for -collapse_cols; added -weight_vec
07 May 2012, DR Glen, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Coordinate transformations in atlas access
Coordinates were not transformed properly if an inverse affine
transformation was required for the case of atlases in another
space than the dataset.
07 May 2012, DR Glen, NIFTI input/output, level 2 (MINOR), type 5 (MODIFY)
NIFTI qform/sform codes from generic space of template space
qform and sform codes are set by string in generic space, not template
space, of input dataset. For example, TT_N27 spaces will be marked for
NIFTI output as TLRC. NIFTI data with any non-ORIG or ACPC space will
be marked as an 'aligned' space in NIFTI with the sform and qform codes.
Currently only TLRC/MNI/Aligned are supported spaces in NIFTI standard.
'aligned' space datasets will be interpreted as equivalent to TLRC view
datasets. See AFNI_atlas_spaces.niml for space definitions that include
generic space names.
07 May 2012, DR Glen, to3d, level 1 (MICRO), type 5 (MODIFY)
Clearer warning for illegal transfer syntax
07 May 2012, DR Glen, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT)
out_space option to force output space for auto-talairached data
04 May 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added inverse distance measures to InstaCorr
For the moment, those options are only accessible to usernames
rwcox and ziad. Relevant functions are:
THD_vectim_distance(), and THD_distance(). THD_distance() is not
used at the moment, it would be from 3dLocalBistat once I get around
to testing it. For now, its access from 3dLocalBistat is #if-ed out.
04 May 2012, RW Cox, 1dBport, level 1 (MICRO), type 2 (NEW_OPT)
Add -quad option = linear and quadratic trend regressors
04 May 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 4 (BUG_FIX)
submitting updates from Rayus
Updates are in changelog.
03 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -backward_diff and -forward_diff
Note, -backward_diff is the same as -derivative.
02 May 2012, RW Cox, coxplot, level 1 (MICRO), type 0 (GENERAL)
More minor changes to timeseries plotting
Rounded joins for lines drawn in 'new' mode. Use new mode for final
rendering in plug_realtime.c (but not for realtime graphing). Etc.
02 May 2012, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
added AFNI_PATH_SPACES_OK, for input of datasets with spaces in path
Added for V Roopchansingh.
01 May 2012, RW Cox, mri_stats, level 1 (MICRO), type 4 (BUG_FIX)
Fixed student_t2z problem with very tiny p values (roundoff error)
01 May 2012, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE)
allowed -ordered_stimuli and -max_consec, together
Requested by Liat.
01 May 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
added -prefix option; added censor coloring to 1dplot commands
01 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
added -looks_like_AM
30 Apr 2012, RW Cox, 1dplot, level 1 (MICRO), type 0 (GENERAL)
Add anti-aliasing rendering to X11 drawing as well.
Set AFNI_1DPLOT_RENDEROLD to YES to turn this feature off (but why?).
30 Apr 2012, RC Reynolds, afni_restproc.py, level 3 (MAJOR), type 1 (NEW_PROG)
this program is by Rayus Kuplicki, please contact him for information
27 Apr 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added percentile thresholding to AFNI's interface
Relevant functions:
flush_vinfo_sort();
flush_3Dview_sort();
get_3Dview_sort();
AFNI_thresh_from_percentile()
Relevant structure variables:
cont_perc_thr in Three_D_View;
th_sort, N_th_sort, th_sortid in AFNI_view_info;
Feature also accessible from plugout_drive with: SET_FUNC_PERCENTILE +/-
27 Apr 2012, RW Cox, 3dANOVA and 3dRegANA, level 1 (MICRO), type 0 (GENERAL)
Modified to use a random SUFFIX for temp filenames
To avoid conflict when running 2+ copies in the same directory. Per the
request of Tom Holroyd.
27 Apr 2012, RW Cox, 1dplot, level 1 (MICRO), type 0 (GENERAL)
Modify rendering of images (jpeg, png) to look nicer
27 Apr 2012, RC Reynolds, 3dmask_tool, level 3 (MAJOR), type 1 (NEW_PROG)
a program to manipulate mask datasets
26 Apr 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Made header_name be same as brik_name for NIFTI dsets
Changes were in EDIT_dset_items(), search for April 26
26 Apr 2012, RW Cox, 3dLocalBistat, level 2 (MINOR), type 2 (NEW_OPT)
Allow 1 volume vs. multi-volume; Add slope options
25 Apr 2012, RW Cox, 3dNormalityTest, level 1 (MICRO), type 2 (NEW_OPT)
Add -pval option, to get a 'pure' p-value out
24 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Can read .niml.tract files as DOs. Nothing too fancy yet
Tractography files are loaded and handled like any DO.
See function SUMA_DrawTractDO().
24 Apr 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Wrote TrackIO.[ch] to handle tractography data I/O.
All changes are under ptaylor/ . New tract format is in NIML.
See functions in TrackIO.h for details.
24 Apr 2012, ZS Saad, 3dTrackID, level 2 (MINOR), type 5 (MODIFY)
Modified 3dTrackID to make use of new track I/O functions.
24 Apr 2012, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
Add censor stuff to 1dplot, for Colm
24 Apr 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
if surface data with generic prefix, append surf-type suffix
Done to fix ANOVA commands on surface.
Thanks to R Ray for bringing this up.
18 Apr 2012, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
Patch BLOCK and dmBLOCK to have their old non-unit-peak behavior
New functions UBLOCK and dmUBLOCK now have the unit-peak behavior.
17 Apr 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
added atlas/ROI label use with <> range selectors (MCW_get_angle_range)
16 Apr 2012, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
New convenience functions for I/O
SUMA_AddDsetIndexCol(), SUMA_CreateFullDsetPointer, and
macro SUMA_DSET_NAME_CHECK Improved name parsing and format guessing.
16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
More I/T selector linkage modes.
16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Show data value at crosshair directly in display
See SUMA_UpdateCrossHairNodeLabelFieldForSO(),
SUMA_FormNodeValFieldStrings(), and SUMA_UpdateNodeValField()
16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Better handling on multiline centering for display in viewer window.
16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
New option to control which node-based DOs are displayed.
See SUMA's interactive help on 'Ctrl+p' for details.
16 Apr 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Created ptaylor/ under src/ to include Paul Taylor's code contributions
To compile all of Paul's programs: cd src/ptaylor; make all
or from src/ make ptaylor_all
Added macros AFNI_3D_to_1D_index and AFNI_1D_to_3D_index in 3ddata.h
16 Apr 2012, ZS Saad, SurfaceMetrics, level 2 (MINOR), type 5 (MODIFY)
Improved output format and added Displayable Objects to output.
16 Apr 2012, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT)
Added -closest_possible
For allowing the substitution of the projection result with
the closest node that could be found along any direction.
See changes to SUMA_GetM2M_NN()
16 Apr 2012, ZS Saad, SampBias, level 2 (MINOR), type 5 (MODIFY)
Improved I/O
16 Apr 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -do_draw_mask to restrict where node-based DOs are shown
16 Apr 2012, ZS Saad, plugout_drive, level 1 (MICRO), type 5 (MODIFY)
Cosmetic error message handling to help debugging SLaconte problems
16 Apr 2012, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY)
Added new help features to bunch of programs
1dCorrelate, 1dTsort, 1ddot, 3dANOVA*, 1dplot, 3dAutobox, cat_matvec,
waver
16 Apr 2012, ZS Saad, afni, level 1 (MICRO), type 4 (BUG_FIX)
Increased allocated space for bigmap variables in display.c
This is to stop a a MCW_malloc post-corruption which happens
under certain compiler/OS combinations. No big deal.
16 Apr 2012, ZS Saad, 1dTsort, level 1 (MICRO), type 2 (NEW_OPT)
Added -imode to return the mode of 1D file content.
16 Apr 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT)
added -regress_bandpass, for bandpass filtering via regression
13 Apr 2012, RC Reynolds, @radial_correlate.py, level 1 (MICRO), type 6 (ENHANCE)
accept +tlrc datasets
12 Apr 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
backport to python 2.2
For files that should work on 2.2, avoid sum() and enumerate().
Thanks to L Broster for reporting problems on python 2.2.
12 Apr 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
backport to python 2.2
09 Apr 2012, DR Glen, whereami, level 1 (MICRO), type 4 (BUG_FIX)
Typo in AFNI_WAMI_MAX_SEARCH_RAD
Wrong name listed in AFNI GUI environment and README.environment
08 Apr 2012, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE)
-ordered_stimuli now takes labels
05 Apr 2012, RW Cox, 3dTnorm, level 2 (MINOR), type 1 (NEW_PROG)
Normalize each time series in a dataset
Like 1dnorm for 3D+time datasets
05 Apr 2012, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT)
Add -zcount option: count number of zero values in a voxel
04 Apr 2012, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
if prefix shows STORAGE_UNDEFINED, use BRIK only if not potential surface
03 Apr 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL)
dmBLOCK now defaults to peak=0 ==> variable amplitude
Former behavior is now achieved with dmBLOCK(1) ==> fixed amplitude.
Also, the peak variable amplitude is now 1, rather than some annoying
value that means nothin to nobody nohow.
03 Apr 2012, RC Reynolds, plug_realtime, level 1 (MICRO), type 5 (MODIFY)
always print the name of the mask dataset in use (via GUI or env)
02 Apr 2012, RW Cox, Lion build, level 1 (MICRO), type 0 (GENERAL)
Modify install process to include useful netpbm program binaries
The stuff that imseq.c uses to write images out (GIF, TIFF, PNG, BMP),
so that fink is not required. Done via Makefile macro
EXTRA_INSTALL_COMMANDS and copying all files in directory EXTRAPROGS to
the output binaries.
02 Apr 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL)
Add MIONN() function to repertoire (negative MION)
30 Mar 2012, RC Reynolds, plug_realtime, level 1 (MICRO), type 5 (MODIFY)
let user know when AFNI_REALTIME_Mask_Dset is applied
30 Mar 2012, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT)
added option -inweight
Added for S Horovitz and S Tinaz.
22 Mar 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Improve display of node-based DOs. ctrl+p for showing subset of objects.
Node-based DOs overwhelm the display. Ctrl+p allows one to show DOs
only around the selected node, or just at it.
See also DriveSuma's -do_mask_mode option.
22 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Add values at node to the display.
This involved an improvement to the centering of text so that
one can center each line in a paragraph
22 Mar 2012, ZS Saad, @Spharm.examples, level 2 (MINOR), type 5 (MODIFY)
Improvements to the script to make it work with new programe versions.
It will now download its own data for demo purporses.
22 Mar 2012, ZS Saad, SurfaceMetrics, level 1 (MICRO), type 2 (NEW_OPT)
Now outputs NIML dsets and Displayable objects for certain metrics
22 Mar 2012, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
apply AFNI_REALTIME_SHOW_TIMES in non-RT feedback case
22 Mar 2012, RC Reynolds, Dimon, level 1 (MICRO), type 6 (ENHANCE)
if RT comm fails with afni, show iochan_error_string()
It occasionally fails at TR=0.125 s.
21 Mar 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 6 (ENHANCE)
look for more motion files; minor changes to output format
21 Mar 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
use run_lengths for TR list; removed path from external motion file
21 Mar 2012, RC Reynolds, 3dcalc, level 1 (MICRO), type 6 (ENHANCE)
added -help description to -help output
To get apsearch to enable completion of -help option.
19 Mar 2012, RW Cox, Makefiles, level 1 (MICRO), type 0 (GENERAL)
Remove -O3 and -ffast-math and -ftree-vectorize from all gcc cases
Too many problems on Lion with -O3 make me suspicious of aggressive
optimization in general.
15 Mar 2012, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
added AFNI_REALTIME_Mask_Dset for per-run control over Mask
Also added some missing vars to README.environment.
Done for J Evans.
14 Mar 2012, RW Cox, AFNI package, level 1 (MICRO), type 0 (GENERAL)
Add Makefile for Mac OS X 10.7 == Lion
No thanks to Apple, by the way -- breaking OpenMP -- what a bunch of
maroons.
14 Mar 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -num_chan and -max_quiet_trs; default sleep = 1.1*TR, max of 2
Added for J Evans and V Roopchansingh.
14 Mar 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
test for global timing before local, as it looks like bad local
Thanks to P Pallett for reporting the problem.
13 Mar 2012, RC Reynolds, lib_qt_gui.py, level 1 (MICRO), type 5 (MODIFY)
has main, so added trivial -help option
12 Mar 2012, RC Reynolds, @SUMA_AlignToExperiment, level 1 (MICRO), type 2 (NEW_OPT)
added -overwrite_resp, so that processing does not have to stop and wait
Also, used 'find' grab *.nii, to fix the failure reported by R Ray.
Forgot to put this in with the afni_proc.py change...
09 Mar 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
added $hemi to rm.mean dset during scaling; added -overwrite_resp to SATE
Surface analysis would fail on 2nd hemi, as rm.mean dset would exist.Also,
added new '-overwrite_resp S' to @SUMA_AlignToExperiement command.
08 Mar 2012, RW Cox, OpenMP program, level 1 (MICRO), type 4 (BUG_FIX)
Replace memcpy/memset with AAmemcpy/AAmemset
OpenMP has trouble with these, particularly on Mac Lion. Files affected
include:
3dAutoTcorrelate.c 3dDespike.c 3dREMLfit.c
3ddata.h cs_qmed.c mri_blur3d_variable.c
mri_nwarp.c mrilib.h rcmat.c
thd_incorrelate.c
AAmemcpy and AAmemset are defined in mrilib.h. In particular, this gets
rid of the vastly annoying ___builtin_object_size undefined symbol error
message when linking an OpenMP program with llvm-gcc-4.2 on Lion.
07 Mar 2012, RW Cox, many, level 1 (MICRO), type 0 (GENERAL)
Many small changes to fix problems caught with the llvm compiler.
07 Mar 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
existing package and install dir no longer required for -defaults
07 Mar 2012, RC Reynolds, GIFTI, level 1 (MICRO), type 4 (BUG_FIX)
fixed sizeof in memset of gim (noted by B Cox)
06 Mar 2012, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Option completion killed filename completion. Not anymore.
06 Mar 2012, RW Cox, 3dNormalityTest, level 2 (MINOR), type 1 (NEW_PROG)
Test voxel values for normality (Gaussianity).
Uses the Anderson-Darling test.
06 Mar 2012, RC Reynolds, uber_subject.py, level 1 (MICRO), type 5 (MODIFY)
move nokia help to -help_install_nokia (since it is not recommended)
05 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Recorder saving was crashing for very long filenames. Not anymore.
The shell however will not like very long names and will complain.
05 Mar 2012, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
Added option auto-completion for AFNI's programs for csh users
The implementation of this feature is via apsearch. In particular,
apsearch -update_all_afni_help now creates the necessary commands
for csh's complete program to know about available options.
See apsearch -help for details.
This was done in conjunction with Brian Pittman.
05 Mar 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
EDIT_empty: only propagate writable storage_modes
Added is_writable_storage_mode and DSET_STORAGE_MODE.
Thanks to Eli for reporting the problem.
05 Mar 2012, RC Reynolds, uber_proc.py, level 1 (MICRO), type 5 (MODIFY)
trivially apply -help option, for apsearch
05 Mar 2012, RC Reynolds, apsearch, level 1 (MICRO), type 5 (MODIFY)
do not set shell variables
02 Mar 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
fixed $runs in multi-run ricor
Thanks to I Mukai for reporting the problem.
01 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed suma crash after a plot a certain plot freeze sequence
The sequence was: create plot, freeze it, get another open
then close the frozen one. At this point, suma lost control
of the still unfrozen one, so it is practically frozen.
Pressing Freeze twice on that remaining plot cause suma to crash.
None of that occurs anymore.
01 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed cutting plane motion while volume rendering under linux
On Macs, the scroll wheel gives out button 6 and 7, on linux
it is Buttons 4 and 5.
01 Mar 2012, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Some cleanups and tweaks of XmHTML library.
Refresh was not working well when scrolling so I ended up adding a mini
refresh routine that seems to do the trick. XmHTMLRefresh(Widget w)
It is called each time there is a repositioning. Perhaps that is overkill,
but no need to sweat this for now.
01 Mar 2012, RW Cox, 1dBport, level 2 (MINOR), type 2 (NEW_OPT)
Several things to keep Rick happy
Option '-band fbot ftop' can now be used more than once.
New option '-nozero' means to NOT include the 0 frequency.
New option '-invert' means to calculate the frequency indexes to remove
from the various '-band' options, then invert them to KEEP only those
frequencies instead. That is, only the frequencies NOT specified via
'-band' will be output in the resultant 1D file.
29 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added option to use html viewer for WAMI results.
This is to allow users to click on a URL if one is available for a certain
atlas result. For now the display is very crude and only accessible with
-DWEBBY_WAMI=YES.
29 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added 'ctrl+W' that allows saving results from interactive correlations.
This allows for convenient saving of interactively created datasets
such as those from single-subject, or group correlation maps in resting
state.
27 Feb 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Allow on the fly definition of standard meshes with -i ld120, for example.
27 Feb 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug in read_niml_file() that incorrectly set a read_header_only flag
27 Feb 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
made a little more intelligent, e.g. make one backup by default
Note: can run this without any existing AFNI binaries, e.g.
@update.afni.binaries -bindir ~/abin -package linux_openmotif
27 Feb 2012, DR Glen, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Bug in combination of multiple affine transformations
Computation error in combining affine transformations
in whereami. Note all default transformations in whereami
do not combine affine transformations. Instead, space
transformations between TLRC and MNI_ANAT spaces are
computed using a 12-piece or a Brett transformation combined
with an affine in two stages.
24 Feb 2012, ZS Saad, general, level 3 (MAJOR), type 5 (MODIFY)
I/O library for R now can use AFNI's c library.
This new functionality allows the use a variety of formats
both surface and volume-based for reading to and writing from R.
3dMEMA can use this new functionality with option -cio
24 Feb 2012, ZS Saad, @RetinoProc, level 2 (MINOR), type 4 (BUG_FIX)
Added number of volume registration regressors to -ort_adjust
24 Feb 2012, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Options -val_diff and -sval_diff to compare values in 2 dsets.
24 Feb 2012, ZS Saad, 3dMEMA, level 2 (MINOR), type 2 (NEW_OPT)
3dMEMA can now handle surface-based data
It makes use of the new I/O functions that use AFNI's
C-library.
24 Feb 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY)
added -moderate_mask, fixed -extreme_mask help
Thanks to R Kuplicki for reporting the help inconsistency.
23 Feb 2012, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Enable 'bigthree' mode for color pbar
If AFNI_PBAR_THREE is YES, the color pbar in the AFNI GUI (but not the
renderer) will start in 'bigthree' mode, with 3 panes -- the colorscale
in the middle one, and the upper and lower panes adjustable to allow for
scaling that is not symmetrical.
22 Feb 2012, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
Compute the mode of ROI voxels, see -mode and -nzmode
22 Feb 2012, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
moved GLOBAL_browser def from afni.h to thd_ttatlas_query.c
- declared in TTQ.h
- deleted #include thd_atlas.h from most .c files
- #include thd_atlas.h in mrilib.h
22 Feb 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -randomize_trs and -seed
Affected 1d_tool.py, afni_util.py, lib_afni1D.py and lib_textdata.py.
21 Feb 2012, RW Cox, 3dAutobox, level 1 (MICRO), type 2 (NEW_OPT)
Add -npad option, for Larry Frank
21 Feb 2012, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE)
if destination directory is not writable, let the user know
21 Feb 2012, DR Glen, whereami, level 4 (SUPER), type 2 (NEW_OPT)
Web-based access atlases available
Able to query web atlases from whereami and open webpages
Support starting with rat brain atlas from Elsevier's
BrainNavigator
17 Feb 2012, RW Cox, debugtrace.h, level 1 (MICRO), type 5 (MODIFY)
Add printout of 'from' and 'to' information on ENTRY/RETURN macros
Also patched up a missing ENTRY macro in new_MCW_optmenu() in bbox.c,
that SOMEONE (who shall go un-named) criminally forgot when patching the
code for LessTif compatibility.
16 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
more quick termination updates
- added -max_images
- do not init vol search state to 2, would limit volumes to 40
- include fl_start in no_wait test
- look for new vol worth of images, but no volume match
14 Feb 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE)
release version 1.0: help, copy tables, scripts imply -no_gui
14 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if -no_wait, terminate on volume_match failure
For F Ye.
13 Feb 2012, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 4 (BUG_FIX)
-orig_vol now forces datum type to be same as that of input.
This fixed a problem with anatomicals ranging in the million(!) to
come up the equivalent of a binary mask with -orig_vol.
13 Feb 2012, RW Cox, 3dPeriodogram, level 1 (MICRO), type 4 (BUG_FIX)
pfact was not static
But apparently worked OK until Ziad initialized it to zero.
10 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Improved snapshot making. Previous bugs were caused by buffer swap problems
This fixed (I hope for good), problems of recording ('r'), continuous
recording (OS X and Linux), and the oversampling.
10 Feb 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE)
added 'paired' toggle box to GUI
10 Feb 2012, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 5 (MODIFY)
tiny help update, as enforced by H Jo
10 Feb 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY)
make tcat files optional; apply prefix to 'basic' commands in driver
10 Feb 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT)
added -check_results_dir for Z Saad
Also, changed -tcat_outlier_warn_limit to -tcat_preSS_warn_limit.
09 Feb 2012, ZS Saad, 3dSurf2Vol, level 2 (MINOR), type 2 (NEW_OPT)
Added -sdata, making 3dSurf2Vol compatible with multitude of surface dsets
08 Feb 2012, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Add ability to flip colors in a discrete paned pbar
And a 'Flip Colors' button to do so.
07 Feb 2012, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT)
Added -out option to handle output in various formats.
Also added -func ALL option.
07 Feb 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -bkg_col and -autorecord options
07 Feb 2012, ZS Saad, 3dcopy, level 2 (MINOR), type 4 (BUG_FIX)
Fixed problem with 3dcopy HHH.nii TTT+orig not producing output
Problem was caused by new change to EDIT_empty_copy() which
assigned storage mode to that of input dset instead of STORAGE_BY_BRICK
Fix involved setting storage mode per the prefix or view in
EDIT_dset_items()
06 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added automatic sub-brick selection matching IxT in interface
Also see corresponding env var: SUMA_IxT_LinkMode
06 Feb 2012, ZS Saad, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
3drefit was failing on the view change when target dset is under a path.
Prolem was with default catenation of path to DSET_BRIKNAME and
DSET_HEADNAME. Those now contain the path automatically.
06 Feb 2012, ZS Saad, 3dANOVA3, level 2 (MINOR), type 4 (BUG_FIX)
Improved (I hope) sub-brick labels. Added FDR too.
Same improvements to all 3dANOVA programs.
06 Feb 2012, ZS Saad, 3dANOVA3, level 2 (MINOR), type 4 (BUG_FIX)
Fixed comaptibility with .niml.dset data
This required more improvements (I hope) to THD_init_diskptr_names() and
EDIT_empty_copy() for surface-based datasets.
06 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
added -no_wait option: never wait for new data
Also, suppress new glob warnings.
Done for F Ye and others.
06 Feb 2012, RC Reynolds, to3d, level 1 (MICRO), type 5 (MODIFY)
tiny help update, as enforced by D Glen
06 Feb 2012, RC Reynolds, 3dsvm, level 1 (MICRO), type 5 (MODIFY)
applied Makefile.INCLUDE updates for J Lisinski and S LaConte
03 Feb 2012, RC Reynolds, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
updated @AddEdge command to match change to afni_base:shell_com
Done with D Glen.
02 Feb 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE)
added basic 3dMEMA capabilities
This affected afni_util.py, ask_me.py, gui_uber_ttest.py, lib_qt_gui.py
lib_subjects.py, lib_uber_ttest.py, uber_subject.py, uber_ttest.py.
01 Feb 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
check for pre-steady state outlier counts
Added option -tcat_outlier_warn_limit.
01 Feb 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 6 (ENHANCE)
check for pre-steady state outlier warnings
31 Jan 2012, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
also update check for '### ASCCONV BEGIN' in to3d...
Problem noted by J Lewis.
31 Jan 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
look for aligned anat _al_junk/keep
31 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_apply_ricor
30 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
ricor block: no longer apply in later 3dDeconvolve
The regressors for slice #0 from the ricor block were being applied in
the final regression (to remove motion) for consistency in degrees of
freedom. But we might rather not do that, particularly since DOF are
not important when proceeding with just correlation coefficients.
30 Jan 2012, RC Reynolds, uber_ttest.py, level 1 (MICRO), type 5 (MODIFY)
all python files use '/usr/bin/env python' instead of '/usr/bin/python'
modified afni_base.py, gui_uber_align_test.py, gui_uber_subj.py,
uber_skel.py, @DoPerRoi.py, gui_uber_skel.py, gui_uber_ttest.py,
uber_ttest.py
28 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
updates for surf analysis of subject FT under AFNI_data6
- added -atlas_followers to @SUMA_AlignToExperiment
- if surf analysis: no scaling mask (e.g. extents)
- updated help example #8 for surf analysis of AFNI_data6 subject FT
28 Jan 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
look for TSNR* in case of surf analysis
27 Jan 2012, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
fix inf loop if some sSliceArray entries not set
Also, now there might be junk between ASCCONV BEGIN and ###, grrrrr...
Problem noted by J Lewis.
26 Jan 2012, ZS Saad, 3dinfill, level 2 (MINOR), type 1 (NEW_PROG)
Fills holes in a volume based on neighboring values
This program is a wrapper to function SUMA_VolumeInFill.
Written in response to a query by Mike Beauchamp.
25 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
back out overzealous -quit changes for now
24 Jan 2012, ZS Saad, SurfExtrema, level 2 (MINOR), type 1 (NEW_PROG)
Finds nodes that are local extrema on the surface.
Program in response to request by Daniel Margulies
23 Jan 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Allowed addition of 'R' or 'L' when jumping to a node.
This make DriveSuma work well with node indices that are specified
for two hemispheres as is done in the batch mode of 3dGroupInCorr.
This applies to both suma and DriveSuma
23 Jan 2012, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Added -ld and -no_ld options
@SUMA_Make_Spec_FS by default now runs MapIcosahedron at two ld values.
23 Jan 2012, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -atlas_followers
Automatically bring along atlas datasets under -surf_anat's directory.
23 Jan 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Improved logic for assigning ROIs when parent is not present
ROI parent assignment now takes into account last visited surfacein any of
the open viewer, and hemisphere side when appropriate.
23 Jan 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug in display of FRAME bound textures.
Looks like it had to do with depth testing.
20 Jan 2012, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT)
Added -h_web, and -Vname= to all C command-line programs.
See also apsearch -web_prog_help option
20 Jan 2012, ZS Saad, afni, level 1 (MICRO), type 5 (MODIFY)
Trim dset names to keep them readable in plugin dataset selector buttons
See function TrimString() and how it is used in PLUG_finalize_dataset_CB()
20 Jan 2012, RC Reynolds, to3d, level 2 (MINOR), type 5 (MODIFY)
mri_read_dicom: if there is no VALID vrCode, skip explicitVR
Done for Chad N.
19 Jan 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Allow definition of DO on the fly with -fixed_do, -mobile_do.
See DriveAfni -help and suma -help_nido
19 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
made -quit more aggressive
18 Jan 2012, ZS Saad, niccc, level 2 (MINOR), type 2 (NEW_OPT)
-s option to test string NI elements
18 Jan 2012, ZS Saad, Surf2VolCoord, level 2 (MINOR), type 2 (NEW_OPT)
-closest_* options to create find nodes that fall closest to XYZ locations
18 Jan 2012, ZS Saad, suma-general, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_Position_Original for controlling initial window position.
Use suma -update_env ; to update env file, then look for
env SUMA_Position_Original for help and default value.
18 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
force anat variable (and children) to be in AFNI format after 3dcopy
Appropriate, and for compatibility with an afni_name.pv change.
17 Jan 2012, ZS Saad, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Allowed BATCH mode to work on surfaces.
17 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
-gert_create_dataset now implies -GERT_Reco and -quit
For Ziad and Daniel.
13 Jan 2012, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT)
Options -pre and -app help in creating filenames regarding of type
12 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed ricor block 3dcalc loop for varying run lengths
11 Jan 2012, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY)
Added copying of label table and atlas point lists to aux copying function
See functions THD_copy_labeltable_atr and THD_copy_datablock_auxdata
for details.
11 Jan 2012, ZS Saad, 3drefit, level 1 (MICRO), type 2 (NEW_OPT)
Added -copytables to copy label tables and atlas point lists
11 Jan 2012, ZS Saad, 3dROIstats, level 1 (MICRO), type 5 (MODIFY)
Use ROI labels in output if label tables or atlas point lists are present
11 Jan 2012, RW Cox, many programs, level 1 (MICRO), type 0 (GENERAL)
Print WARNING message if '-polort A' is used where not allowed
This is the Inati's fault.
11 Jan 2012, RW Cox, 3dhistog, level 1 (MICRO), type 4 (BUG_FIX)
Fix bugs
(a) fbin storing the counts was not always allocated the right length
(b) changed it from int to int64_t to allow for really large datasets
(c) there is no 3rd item
11 Jan 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
dx and dy were reversed in mri_read_dicom.c
Thanks to P Kaskan and F Ye for bringing this up.
10 Jan 2012, ZS Saad, 3dTagalign, level 1 (MICRO), type 2 (NEW_OPT)
Added interpolation options.
10 Jan 2012, RW Cox, 1dBport, level 2 (MINOR), type 1 (NEW_PROG)
Generates sin/cos waveforms for bandpass-via-regression
09 Jan 2012, ZS Saad, suma-general, level 1 (MICRO), type 2 (NEW_OPT)
Added -setenv to all SUMA programs
09 Jan 2012, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT)
Added -setSUMAenv,-N_fore_smooth, and -N_final_smooth
06 Jan 2012, ZS Saad, ROI2dataset, level 1 (MICRO), type 2 (NEW_OPT)
Added -keep_separate to allow for another way to split ROIs
04 Jan 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Automatically add an Atlas to whereami list if encountered in the session
04 Jan 2012, ZS Saad, ROI2dataset, level 1 (MICRO), type 2 (NEW_OPT)
Added -nodelist_with_ROIval to facilitate splitting ROIs
04 Jan 2012, ZS Saad, @Atlasize, level 1 (MICRO), type 2 (NEW_OPT)
Allow for delimiters in keys file and handle names with spaces
Similar additions are made to @MakeLabelTable
04 Jan 2012, RW Cox, 1dsvd, level 1 (MICRO), type 5 (MODIFY)
Add percent ability to -nev option
That is, the ability to output (via -1Dleft) the set of vectors that
make up the first 'n' percent of the column space.
03 Jan 2012, RW Cox, THD_dset_in_session, level 1 (MICRO), type 5 (MODIFY)
Alter FIND_PREFIX to strip off '+view' if present.
30 Dec 2011, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
NIFTI datasets used to loose their path information upon loading.
This is problematic for a few reasons. For instance, afni ~/tmp/joe.niml
will display the dataset as ./joe.niml. Some internal functions for
conveniently dealing with atlases fail when the path is messed up in this
way. Also, this problem occurred for NIFTI but NOT AFNI native formats
wich resulted in different behaviour for programs like 3drefit.
For example: 3drefit -space MNI ~/tmp/joe.nii is not comparable to
3drefit -space MNI ~/tmp/joe+tlrc. (Actually, that behaviour was patched
on Dec 27 but explicitly setting the path at output. But the fix needed
to happen for other programs so that is now done at the io level.)
30 Dec 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Simplified how afni handles custom group or single-subject atlases
By default, SessionAtlases and AFNI_SUPP_ATLAS_DIR/CustomAtlases.niml
are added to the atlas list for whereami queries.
30 Dec 2011, ZS Saad, @MakeLabelTable, level 2 (MINOR), type 2 (NEW_OPT)
Improved @MakeLabelTable's creation of ATLAS niml files
30 Dec 2011, ZS Saad, @Atlasize, level 2 (MINOR), type 1 (NEW_PROG)
A convenience script to turn a dataset to an atlas
The script makes it easy to create a group atlas or a single-subject
atlas and place them automatically in a location that AFNI
recognizes making them available to the user without bothering with
too many environment variable settings.
30 Dec 2011, ZS Saad, @AfniEnv, level 2 (MINOR), type 1 (NEW_PROG)
A convenience script to automatically edit .afnirc
30 Dec 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Numerous new options to 3dinfo, including checks for dset presence on disk
27 Dec 2011, ZS Saad, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
3drefit failed when refitting a NIFTI dset in another directory.
If you did something like 3drefit -space MNI joe/jim/dset.nii
you ended up with a new dataset ./dset.nii as opposed to modifying
the one under joe/jim/ directory
23 Dec 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Allow user to append a string to the overlay label
Via environment AFNI_IMAGE_LABEL_STRING or by a new item on the
intensity bar popup menu in the GUI -- the latter takes precendence.
This is Ziad's Xmas present.
22 Dec 2011, RW Cox, mycat, level 1 (MICRO), type 1 (NEW_PROG)
Minor program to be sort of like 'cat' but un-Microsofts files.
22 Dec 2011, RW Cox, afni_fgets, level 1 (MICRO), type 5 (MODIFY)
Modified to use system fgets if file pointer is a ttty
22 Dec 2011, RW Cox, afni realtime plugin, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_REALTIME_External_Dataset environment variable
Lets the realtime user (let's call her/him 'CC') specify an external
dataset to be used as the registation base. CC doesn't have to use a
dataset that is in the cwd, unlike the plugin's GUI selector. Nor does
the setting of this environment variable affect the plugin's GUI.
21 Dec 2011, RW Cox, afni_fgets, level 1 (MICRO), type 5 (MODIFY)
Modify to use system fgets for stdin
20 Dec 2011, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
SUMA now allows for direct recording to disk.
See SUMA's ctrl+h for key ctrl+R for details.
Related environment variable is SUMA_AutoRecordPrefix.
20 Dec 2011, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
SUMA now displays area labels in the viewer, F9 key toggles it
See SUMA's ctrl+h output in the section for F9
Related environment variable is SUMA_ShowLabelsAtCrossHair.
20 Dec 2011, ZS Saad, 3dclust, level 2 (MINOR), type 4 (BUG_FIX)
-prefix failed when input dset was mastered.
Better use macro PREP_LOADED_DSET_4_REWRITE whenever modifying
a dataset loaded from disk for the purporse of rewriting it.
20 Dec 2011, ZS Saad, 3dUpsample, level 2 (MINOR), type 2 (NEW_OPT)
Allow for upsampling to go to 11 (actually 320) and control output datum
20 Dec 2011, RW Cox, fgets, level 1 (MICRO), type 0 (GENERAL)
Replace (mostly) fgets with afni_fgets
Recognizes CR and CR+LF and LF+CR as line enders, not just LF like the
standard Unix library function -- these Microsofties are killing me.
20 Dec 2011, RW Cox, fdrval, level 1 (MICRO), type 5 (MODIFY)
Add -inverse (AKA -qinput) option
Allows user to compute the threshold, given the q-value.
20 Dec 2011, RW Cox, 3dttest++, level 1 (MICRO), type 5 (MODIFY)
Add debug output to thd_table.c
To help me (and users) figure out what might be wrong with a covariates
table. Also applies to 3dGroupInCorr
19 Dec 2011, RW Cox, THD_patch_brickim, level 1 (MICRO), type 5 (MODIFY)
Modify to set zero dataset grids spacings to a nonzero value
In the dataset struct itself, that is, not just the brick image structs.
16 Dec 2011, RW Cox, 3dLSS, level 1 (MICRO), type 0 (GENERAL)
Added -nodata option, and fleshed out the help with an example.
15 Dec 2011, RW Cox, 3dLSS, level 1 (MICRO), type 1 (NEW_PROG)
3dLSS implement LS-S regression
As described in Mumford, Turner, Asby, and Poldrack, NeuroImage 2011.
See 3dLSS -help for more info.
13 Dec 2011, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
-init_xform to allow for an initial transformation of -surf_anat
13 Dec 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
-same_* options return information about dset pairs
13 Dec 2011, ZS Saad, plugout_drive, level 1 (MICRO), type 4 (BUG_FIX)
AFNI_drive_switch_* functions discriminated against short prefixes.
12 Dec 2011, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT)
Small improvements and addition of logging option of search results
See -apsearch_log_file option for details. Logging is only enabled
if AFNI_LOG_BEST_PROG_OPTION is set to YES.
12 Dec 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Slice displays can now show atlas labels in addition to slice location
The displays are turned on by right-clicking on the slice viewer's color
bar and then setting the 'Label' to something other than 'OFF'
See isqCR_getlabel, ISQ_getlabel, and AFNI_get_dset_val_label in code
12 Dec 2011, ZS Saad, @global_parse, level 2 (MINOR), type 1 (NEW_PROG)
Script to simplify support of global options such as h_find from scripts
09 Dec 2011, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_DoNotSendStates restricts certain surfaces from getting sent to suma.
09 Dec 2011, RW Cox, afni (imseq.c), level 1 (MICRO), type 4 (BUG_FIX)
Patch weird bug
When the intensity bar popup menu is up, then the user clicks on an
optmenu, then the next time the user button1 clicks in the image viewer
(say to move the crosshairs), the values of last_bx and last_by are lost
(reset to 0) so the move wrong. Solution -- check if button release is
in the same location (or close) as the button press, and only then allow
a move.
09 Dec 2011, RW Cox, 3dttest, level 1 (MICRO), type 4 (BUG_FIX)
Fix sub-brick selection bug
in THD_multiplex_dataset(), the '$' was not treated right -- just set to
999998. Fix is to use MCW_get_thd_intlist() for proper expansion, which
also will add sub-brick label selection capability.
07 Dec 2011, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Added atlas creation of aseg, aparc+aseg, in addition to aparc.a200*
See whereami's example 3 for how to extract ROIs from FreeSurfer atlases.
07 Dec 2011, ZS Saad, @FS_roi_label, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug caused by not cleaning tmp files under /tmp/ with -rankmap
This bug should not have affected anyone. It showed up as I
was making @SUMA_Make_Spec_FS process more than one type of
parcellation volume.
06 Dec 2011, ZS Saad, apsearch, level 1 (MICRO), type 2 (NEW_OPT)
-stdin for input
More tweaking of search distances and a battery of tests
to help decide if tweak is in the right direction.
06 Dec 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL)
Allow runs with -polort ONLY (no other regression model)
05 Dec 2011, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT)
Added -h_view to all C command-line programs.
See also apsearch -view_prog_help option
05 Dec 2011, ZS Saad, afni-general, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_GUI_EDITOR controls user's preferred text editor.
See apsearch -afni_text_editor.
02 Dec 2011, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT)
-XYZscale is added to scale the coordinates of a surface
Surface that are not in mm coordinates can look pretty bad in SUMA.
This scaling option can be used to easily change coordinates from cm to mm
for example.
02 Dec 2011, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT)
Added 'Save' button to suma text info windows
02 Dec 2011, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_NodeCoordsUnits allows the specification of node coord. units
02 Dec 2011, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Wrote SOLARIS_strcasestr to replace missing strcasestr on SOLARIS
02 Dec 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT)
Add -ortvec option (to appease the Inati)
Lets the pitiful user add multiple baseline (i.e., ort) vectors from a
single file.
01 Dec 2011, RW Cox, p2t, level 1 (MICRO), type 0 (GENERAL)
Remove this program from AFNI binary distributions
30 Nov 2011, ZS Saad, ConvertDset, level 1 (MICRO), type 2 (NEW_OPT)
-pad_to_node 0 now padds output dset to max node in input dset
29 Nov 2011, ZS Saad, @clean_help_dir, level 1 (MICRO), type 1 (NEW_PROG)
Removes redundant help files from the afni help directory.
29 Nov 2011, ZS Saad, @DeblankFileNames, level 1 (MICRO), type 1 (NEW_PROG)
Replaces spaces in filenames with_something_less_annoying.
28 Nov 2011, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Fixed function THD_deplus_prefix to improve prefix cleanup
Previous version cleaned +orig but not +orig.HEAD or +orig. for example.
Current one removes +orig +orig. +orig.HEAD +orig.BRIK +orig.BRIK.gz and
corresponding +acpc and +tlrc brethren.
28 Nov 2011, RC Reynolds, 1dnorm, level 1 (MICRO), type 4 (BUG_FIX)
re-enabled use of '-' for stdin/stdout
Requested by R Birn.
25 Nov 2011, ZS Saad, to3d, level 1 (MICRO), type 2 (NEW_OPT)
Added -quit_on_err
Keeps to3d from going in interactive mode in case of error.
25 Nov 2011, ZS Saad, Dimon, level 1 (MICRO), type 2 (NEW_OPT)
Added -gert_quit_on_err
Passes -quit_on_err option to to3d.
22 Nov 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT)
Added -h_find as a global option
afni -help now outputs information about 'Global options'
22 Nov 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT)
allow for passing variables directly, not via -svar
21 Nov 2011, ZS Saad, apsearch, level 1 (MICRO), type 2 (NEW_OPT)
Added -all_opts to show all options for a program
21 Nov 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT)
Added -all_opts as a global option
The option is the equivalent of running apsearch -all_opts
for a certain program.
21 Nov 2011, RC Reynolds, quick.alpha.vals.py, level 2 (MINOR), type 1 (NEW_PROG)
a very simple program to tabulate the output from slow_surf_clustsim.py
This ought to be improved, but at least it is now distributed...
21 Nov 2011, RC Reynolds, uber_subject.py, level 1 (MICRO), type 6 (ENHANCE)
small update to help text
21 Nov 2011, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed -ynames in plot of motion/outliers
18 Nov 2011, RW Cox, 3dUndump, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug introduced with -ROImask
17 Nov 2011, ZS Saad, apsearch, level 2 (MINOR), type 1 (NEW_PROG)
This is a program to test approximate string matching functions
The program is best described by its help output.
It is meant to quickly test the behavior of the approx* functions
in thd_ttatlas_query.c where approximate string matching will
be useful is easily specifying an atlas areas by name.
Another useful offshoot is the function: suggest_best_prog_option
which can easily be called right after a command-line parsing error
message is displayed. For example, in apsearch I have the following:
{ /* bad news in tennis shoes */
fprintf(stderr,"** Error %s: bad option %s\n", argv[0], argv[iarg]);
suggest_best_prog_option(argv[0], argv[iarg]);
return 1;
}
So all is needed to retrofit an old program is the suggest function.
That function will do nothing if environment variable AFNI_NO_OPTION_HINT
is set.
To use suggest_best_prog_option from a script, use:
apsearch -popt `basnemane $0` -word ARG
17 Nov 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
If AFNI_NO_OPTION_HINT, don't bother with helpful suggestions
17 Nov 2011, ZS Saad, afni, level 1 (MICRO), type 3 (NEW_ENV)
Added threshold locking capability under the 'Lock' menu
17 Nov 2011, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
if dset+orig is anat/func and dset+tlrc is func/anat, 'BAD dataset', man
Altered logic in thd_initsess.c (done with dglen).
17 Nov 2011, RC Reynolds, @ROI_Corr_Mat, level 1 (MICRO), type 4 (BUG_FIX)
fix complaint about unknown options for non-macs
17 Nov 2011, RC Reynolds, 3drefit, level 1 (MICRO), type 4 (BUG_FIX)
changing 'type' should have an effect even if not a bucket
Done with dglen.
16 Nov 2011, RW Cox, dicom_hinfo, level 1 (MICRO), type 0 (GENERAL)
Minor edits, mostly to the help.
16 Nov 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
Condition numbers were checked with SQUARES of singular values!
Fixed by changing function matrix_singvals(). Also make clear in 1dsvd
help that -vnorm option is needed to compare singular values with
3dDeconvolve.
15 Nov 2011, ZS Saad, afni_general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug introduced by cleaning up header_name and brick_name
15 Nov 2011, ZS Saad, afni_general, level 2 (MINOR), type 4 (BUG_FIX)
More changes regarding obliquity warnings.
AFNI:
Popups only appear when user is viewing dsets of different obliquity.
See dset_obliquity_angle_diff()
and THD_report_obliquity()
The warnings only appear ONCE per pair of misfits, per afni process.
See AFNI_check_obliquity() for implementation details.
Oblique notices no longer appear on the command line each time you
read a session or switch dsets. To tell you that you are viewing an
oblique dset and that the coords are not quite what they should be,
I added a '*' next to the 'order:' descriptor in the top left corner.
Command Line programs:
In most programs that should not care about obliquity, I add
early under main():
set_obliquity_report(0); /* silence obliquity */
Also, 3dcalc, 3dTcat, 3dbucket, and function THD_open_tcat()
Only complain when obliquity between dset pair differs.
The check is done right after checking for grid matching with
EQUIV_DATAXES
15 Nov 2011, RW Cox, dicom_hinfo, level 2 (MINOR), type 1 (NEW_PROG)
For printing out info from lots of DICOM files
For each file input, prints 1 line with the values of only the desired
tags. The goal is to be helpful in figuring out which files go
together. See Example #2 in the help output for such a case.
10 Nov 2011, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Turned off obliquity popup warning when Ulay and Olay angles are similar
AFNI issues warning when obliquity differs for a pair of viewed sets.
It does not repeat warnings for a certain pair. It only output one set
of warnings per dataset when 'switch ulay' is set, although I'd love to
get rid of that habit as soon as possible.
10 Nov 2011, ZS Saad, 3dinfo, level 1 (MICRO), type 4 (BUG_FIX)
Many new options for selective information.
10 Nov 2011, RW Cox, afni InstaCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add ExtraSet option
That is, to correlate seeds from the TimeSeries dataset with voxel data
from the ExtraSet dataset. Ziad asked for something like this, so here
it is.
09 Nov 2011, RW Cox, 3dUndump, level 2 (MINOR), type 2 (NEW_OPT)
Add -ROImask option
To put values into locations defined by a mask dataset.
09 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
-surf_blur_fwhm is no longer valid, please use -blur_size
08 Nov 2011, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_IMAGE_COLORANGLE
Set this to 360 to get the 'Colr' image to be a full circle colormap.
08 Nov 2011, RC Reynolds, adwarp, level 1 (MICRO), type 6 (ENHANCE)
added a help example for writing anat+tlrc.BRIK
07 Nov 2011, RW Cox, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
No -iresp or -sresp for dmBLOCK
Also, change defintion of 'near-duplicate' times from 0.05*TR to 0.50*TR
07 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -blur_to_fwhm and -blur_opts_B2FW
Added for E Nelson and J Jarcho.
07 Nov 2011, DR Glen, lost last character in sub-brick labels, level 2 (MINOR), type 4 (BUG_FIX)
Fixed miscount of characters
07 Nov 2011, DR Glen, deobliquing, level 2 (MINOR), type 5 (MODIFY)
More programs lose original data obliquity
3drefit, 3dWarp, 3daxialize, 3dZcutup, 3dCM, 3dZregrid
added to the list of programs
04 Nov 2011, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 6 (ENHANCE)
added 'mode' mapping function
Requested by R Mruczek. Also done for Z Puckett.
03 Nov 2011, RC Reynolds, @2dwarper.Allin, level 2 (MINOR), type 2 (NEW_OPT)
added -prefix option; allow for 3dAllin failures; copy time info
Updates by N Mei and A Messinger.
03 Nov 2011, DR Glen, longer sub-brick labels, level 2 (MINOR), type 5 (MODIFY)
Allow sub-brick labels to be up to 63 characters
03 Nov 2011, DR Glen, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Allow refitting of some attributes
Some attributes like IJK_TO_DICOM_REAL and DELTA were not
being updated correctly with the original values remaining
in the dataset
02 Nov 2011, ZS Saad, 3dfim+, level 1 (MICRO), type 4 (BUG_FIX)
Turned off scaling for Best Index in output dset
02 Nov 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
added out.TENT_warn.txt to warning file review
02 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
if using TENT, run 'timing_tool.py -warn_tr_stats'
Warnings are also saved in out.TENT_warn.txt.
02 Nov 2011, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
allow -save_file_list to apply even with -infile_list
31 Oct 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_tr_stats and -warn_tr_stats options
26 Oct 2011, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT)
Made SUMA hide overlay from SUMA whenever 'See Overlay' is off in AFNI
26 Oct 2011, ZS Saad, afni, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug where AFNI sent the max voxel to suma despite threshold
In BYTE and SHORT datasets the maximum voxel always got sent to
suma, even if the threshold was higher than the maximum value in
the dataset.
25 Oct 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE)
process married files with current operations
1. AfniMarriedTiming inherits from AfniData (instead of local copies)
2. add all AfniTiming methods to AfniMarriedTiming (as married timing)
3. rename AfniMarriedTiming back to AfniTiming (but now married)
25 Oct 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
look for more file name variants, including with '_' separators
Added for J Weisberg.
20 Oct 2011, RC Reynolds, afni_general, level 2 (MINOR), type 5 (MODIFY)
changed most resampling programs to deoblique inputs upon read
THD_open*_dataset() was followed by THD_make_cardinal().
modified: 3dresample, 3dfractionize, 3drotate, adwarp, 3dLRflip
3dZeropad, 3dZcat, 3dAutobox
not (yet) modified: 3dWarp(Drive), 3dAllineate
19 Oct 2011, RC Reynolds, GIFTI, level 2 (MINOR), type 6 (ENHANCE)
can read/write ascii COMPLEX64, COMPLEX128, RGB24
Requested by H Breman, J Mulders and N Schmansky.
19 Oct 2011, RC Reynolds, @2dwarper.Allin, level 1 (MICRO), type 2 (NEW_OPT)
added a -mask option
Added for A Messinger.
18 Oct 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT)
Added -available_npb* options to suggest available port blocks
18 Oct 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT)
added blur size control; removed requirement of stim timing files
18 Oct 2011, RC Reynolds, @radial_correlate, level 1 (MICRO), type 6 (ENHANCE)
require enough volumes per dataset, store file name correspondence
17 Oct 2011, RW Cox, 3dhistog, level 1 (MICRO), type 5 (MODIFY)
removed DOS ctrl-M's in file, they screwed things up for compiling
17 Oct 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
added -help for new -surf_* options, along with example #8
17 Oct 2011, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY)
abin now has subdir (funstuff), so change 'mv' to 'rsync'
14 Oct 2011, ZS Saad, afni-general, level 2 (MINOR), type 0 (GENERAL)
Improvements of atlas handling in whereami and afni
1- In addition to loading atlas specs from environment variable
AFNI_SUPP_ATLAS, AFNI will automatically search for a file
named SessionAtlases.niml which is created with @MakeLabelTable.
2- AFNI will check if a viewed dataset is an atlas and will
automatically add it to the atlas list. It will also show the label at
the cross-hair location.
New functions of interest:
get_Atlas_ByDsetID, is_Dset_Atlasy,
label_table_to_atlas_point_list, is_identity_xform_chain
14 Oct 2011, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
now processes surface data
- added 'surf' processing block, and corresponding '-surf_*' options:
-surf_anat, -surf_spec, -surf_anat_aligned, -surf_anat_has_skull,
-surf_A, -surf_B, -surf_blur_fwhm
- compute errts and TSNR by default (had required option or blur est)
14 Oct 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
allow modest handling of surface results
14 Oct 2011, RC Reynolds, uber_subject.py, level 1 (MICRO), type 6 (ENHANCE)
small -help_install update
13 Oct 2011, ZS Saad, whereami, level 2 (MINOR), type 4 (BUG_FIX)
-omask failed if atlas was stored in float type.
13 Oct 2011, ZS Saad, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Added support for -atrstring operation on NIFTI datasets
This required making changes to THD_init_diskptr_names functions
and a few more of its colleagues.
13 Oct 2011, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fixed error in computing with un-centered covariates
inv[Xt*X] matrix not computed correctly in mri_matrix_psinv_pair()
function.
12 Oct 2011, RW Cox, NIML library, level 1 (MICRO), type 0 (GENERAL)
Extend printout of floats to higher precision
11 Oct 2011, ZS Saad, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT)
Added support for NIFTI datasets
11 Oct 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Added new options for extracting field values in scripts
07 Oct 2011, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Move splashes, faces, and poems to funstuff/ subdirectory
funstuff/ is now a sub-directory of the binary install directory.
07 Oct 2011, RW Cox, 1dTsort, level 1 (MICRO), type 0 (GENERAL)
Add -col option, to sort on just one column.
06 Oct 2011, RC Reynolds, 3dMean, level 1 (MICRO), type 4 (BUG_FIX)
linux_xorg7_64 had optimizer error (and crashed), so altered loop method
Thanks to P Kim for reporting the problem.
05 Oct 2011, RC Reynolds, uber_subject.py, level 1 (MICRO), type 4 (BUG_FIX)
do not re-create proc script on proc execution
04 Oct 2011, ZS Saad, GroupAna, level 2 (MINOR), type 2 (NEW_OPT)
Added support for writing NIML files as output
This also required writing a few new matlab functions such as
BrikInfo_2_niml_writesimple.
04 Oct 2011, ZS Saad, CreateIcosahedron, level 1 (MICRO), type 2 (NEW_OPT)
Added -min_nodes option
04 Oct 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
changed basic script outputs
- added 'max censored displacement', 'final anat dset' and
'final voxel resolution' to basic script
- removed 'num stim files found'
04 Oct 2011, RC Reynolds, to3d, level 1 (MICRO), type 5 (MODIFY)
explicitly warn about illegal '/' characters in output filename
04 Oct 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT)
added -anat_has_skull option
03 Oct 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -censor_infile (e.g. to remove TRs from motion params)
Added for N Adleman.
03 Oct 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
changed default polort time back to TR*NT, to match 3dDeconvolve
03 Oct 2011, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
update ADN_ONE_STEP to ten million, allowing that many output sub-bricks
This affects programs like 3dbucket, when the output has many volumes.
Done for HJ Jo, J Gonzalez-Castillo, M Robinson.
22 Sep 2011, RC Reynolds, uber_ttest.py, level 3 (MAJOR), type 1 (NEW_PROG)
a graphical program for running either 3dttest++ or 3dMEMA
Still under destruction.
22 Sep 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 5 (MODIFY)
altered spacing and made other minor changes
22 Sep 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY)
added check_for_file and for_dset, updated find_x_mat, enorm, view_stats
22 Sep 2011, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
various updates
- updated quotize_list
- added nuke_final_whitespace, flist_to_table_pieces, get_ids_from_dsets
22 Sep 2011, RC Reynolds, uber_align_test.py, level 1 (MICRO), type 5 (MODIFY)
moved get_def_tool_path to library
21 Sep 2011, RW Cox, 3dTshift, level 1 (MICRO), type 2 (NEW_OPT)
Add -voxshift option
21 Sep 2011, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT)
Add -2sided option
13 Sep 2011, DR Glen, 3dMean, level 2 (MINOR), type 2 (NEW_OPT)
Added non_zero and count options
13 Sep 2011, DR Glen, whereami, level 1 (MICRO), type 4 (BUG_FIX)
Added trivial ability to invert identity transformation
07 Sep 2011, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY)
added @radial_correlate to the install scripts (forgot earlier)
06 Sep 2011, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT)
added -fast option, short for: -sleep_init 50 -sleep_vol 50
06 Sep 2011, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
save_skullstrip option saved obliqued and skullstripped data
Fixed to save only skullstripped
02 Sep 2011, DR Glen, 3dhistog, level 2 (MINOR), type 4 (BUG_FIX)
Handle binning and output of integer and float data differently
Distinguish between integer and float data. Added float and int
options to enforce specified behavior.
Done with Rick Reynolds.
01 Sep 2011, RC Reynolds, @radial_correlate, level 2 (MINOR), type 1 (NEW_PROG)
compute voxelwise EPI correlations with local spherical averages
01 Sep 2011, RC Reynolds, afni_util.py, level 1 (MICRO), type 4 (BUG_FIX)
get_default_polort: run time should be TR * (NT-1)
This was changed back to TR*NT, to match 3dDeconvolve (3 Oct, 2011).
31 Aug 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
if censoring motion or outliers, add options to gen_ss_r command
30 Aug 2011, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
update volume delta to mean dz
From text in DICOM files, initial dz values may not be sufficiently
accurate, leaing to 'volume toasted' errors.
Thanks to B Benson for reporting the problem.
30 Aug 2011, DR Glen, Draw Dataset, level 2 (MINOR), type 4 (BUG_FIX)
Draw Dataset plugin incorrect label for current atlas
Fixed current atlas to be updated properly if atlas is
changed.
26 Aug 2011, RW Cox, afni Clusterize, level 1 (MICRO), type 0 (GENERAL)
Modify to print out 3dclust and whereami commands when used
Per the suggestion of Andy Connolly of Dartmouth College.
26 Aug 2011, RW Cox, 3dclust, level 1 (MICRO), type 2 (NEW_OPT)
add -savemask option
19 Aug 2011, RW Cox, 3dNwarpCalc, level 2 (MINOR), type 5 (MODIFY)
Fix &readpoly() and implement &read4x4()
Modify 3dNwarpApply to use same function as &apply() so that the 2
programs are in sync.
Release 3dNwarpCalc into the wild:
Born free, and code is worth running, but only worth running, because
you're born freeware!
19 Aug 2011, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
added the ability to output 1D sresp datasets
Requested by S Baum.
18 Aug 2011, RW Cox, 3dttest++, level 1 (MICRO), type 0 (GENERAL)
Add some clarify text about covariates to the -help output
Also add an addition check to see if dataset name covariates are all the
same, and print out some info about the covariates.
18 Aug 2011, RW Cox, 3dNwarpCalc, level 1 (MICRO), type 0 (GENERAL)
Add '&apply' function
To apply a calculated 3D warp to a dataset, without having to use
3dNwarpApply
17 Aug 2011, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed some final anat dset assignments
15 Aug 2011, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
altered SUMA_ParseFname for parsing of relative pathnames
Thanks to Ryan of Princeton for reporting the problem.
12 Aug 2011, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY)
gave volreg 3dAllineate command priority for final anat
11 Aug 2011, RW Cox, 3dNwarpCalc, level 1 (MICRO), type 0 (GENERAL)
Added sqrt of a nonlinear warp to the repertoire.
09 Aug 2011, RW Cox, 3dNwarpCalc, level 2 (MINOR), type 1 (NEW_PROG)
Implemented about 80% of it
Seems to work, but needs a fair amount of fine tuning and testing.
09 Aug 2011, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT)
Add '-cvarinv' option for Vinai
04 Aug 2011, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
wrote loc_strcpy(/cat)_realloc for MCW_file_expand
This is to allow for long sub-brick selectors.
03 Aug 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
changed aea.py -save_skullstrip to -save_orig_skullstrip
The -save_skullstrip dataset might have an oblique transformation
applied (which would throw off EPI if it is then sent to standard
space). Apply the new option to grab a simple skull-stripped anat.
Thanks to A Ellenstein for reporting it and Z Saad for help understanding.
03 Aug 2011, RC Reynolds, align_epi_anat.py, level 1 (MICRO), type 2 (NEW_OPT)
added -save_orig_skullstrip, to avoid oblique transforms
This was added for afni_proc.py.
02 Aug 2011, RW Cox, 3dclust, level 2 (MINOR), type 2 (NEW_OPT)
Add '-inmask' option, to use internal mask
To be compatible with AFNI's Clusterize GUI, which was also modified to
output this option when appropriate.
02 Aug 2011, RC Reynolds, uber_skel.py, level 1 (MICRO), type 5 (MODIFY)
main class inherits object - for older versions of python
02 Aug 2011, RC Reynolds, uber_align_test.py, level 1 (MICRO), type 5 (MODIFY)
main class inherits object - for older versions of python
02 Aug 2011, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY)
added control var out_prefix, a prefix for output files
01 Aug 2011, ZS Saad, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Whereami's symbolic notation failed with float valued atlases
This is now fixed. Code also checks for scale factors.
There was another bug waiting to happen with:
!is_Atlas_Named(atlas, "CA_N27_PM"), which is now:
!is_probabilistic_atlas(atlas)
01 Aug 2011, ZS Saad, Draw Dataset, level 2 (MINOR), type 5 (MODIFY)
Changed the gap selection to arrows to allow for much larger gaps
01 Aug 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Clusterize minor changes
* Shift+3clust button = actually run the 3dclust command, in addition
printing it out
* Add a warning message if an internal 3dClustSim mask is present, since
3dclust results will vary from Clusterize
* Add Jumpto buttons to AFNI crosshair label popup menu
29 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 6 (ENHANCE)
z.max files are now named by p-value
And suggest a quick.alpha.vals.py command.
29 Jul 2011, RC Reynolds, make_pq_script.py, level 2 (MINOR), type 5 (MODIFY)
changes to handle python 2.4, where shell output has extra blank lines
29 Jul 2011, RC Reynolds, 3dUniformize, level 2 (MINOR), type 4 (BUG_FIX)
fixed checks against lower_limit in option processing (since -1 init)
Thanks to A Waite for reporting the problem and cause in the code.
26 Jul 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
if e2a, update current anat to skull-stripped anat from align block
This would avoid a second skull-strip step in @auto_tlrc.
25 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 6 (ENHANCE)
added keepblocks var, to limit kept intermediate datasets
22 Jul 2011, ZS Saad, afni, level 1 (MICRO), type 3 (NEW_ENV)
Added AFNI_TIME_LOCK to turn on AFNI's Time Lock by default
22 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 4 (BUG_FIX)
after blur, rescale noise to be normally distributed
21 Jul 2011, RW Cox, 3dttest++, level 1 (MICRO), type 5 (MODIFY)
Add column selection to -covariates for this, also
21 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY)
changed TR counts to come via awk instead of grep
21 Jul 2011, RC Reynolds, edt_blur.c, level 1 (MICRO), type 4 (BUG_FIX)
fixed nz/sigmay typo, found by Patryk (on message board)
20 Jul 2011, ZS Saad, 1dcat, level 1 (MICRO), type 2 (NEW_OPT)
added -sel option to 1dcat
with -sel one can apply the same selection of columns and rows
to all files on the command line, allowing the use of wildcards
when specifying input 1D files.
20 Jul 2011, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 5 (MODIFY)
Allow sub-brick selectors on the -covariates table
20 Jul 2011, RC Reynolds, make_pq_script.py, level 2 (MINOR), type 1 (NEW_PROG)
program will generate a script to produce a p-value/q-value curve pair
20 Jul 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed aea.py -epi_base when: aea.py, -volreg_a2 last, variable run lens
thanks to S Brislin and S White for reporting the problem
15 Jul 2011, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 2 (NEW_OPT)
Add -center option for covariates (cf. Chen Gang)
15 Jul 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
save output from ss_review in out.ss_review.$subj.txt
15 Jul 2011, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE)
applied -d as -defaults
14 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
added 'max motion displacement' to basic script
14 Jul 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_max_displace, for maximum motion displacement
14 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 6 (ENHANCE)
show date per iter block and add ./ to 3dcalc prefix
13 Jul 2011, RW Cox, 3dTcorrMap, level 2 (MINOR), type 4 (BUG_FIX)
Bug in computation of indx
The mask is turned into an index table of active voxel indx[]. However,
constant voxels were removed from the mask AFTER indx[] was created,
which is stupid. This is fixed now, and Zhark will be chastised.
13 Jul 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
run gen_ss_review_scripts.py and any resulting 'basic' review script
13 Jul 2011, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 2 (NEW_OPT)
added -exit0 and babbled about possible artifact tests
11 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 3 (MAJOR), type 1 (NEW_PROG)
for generating single subject review scripts
To be run by the afni_proc.py proc script or directly by users.
11 Jul 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed case of partial path match to dsets
Problem found by J Jarcho.
11 Jul 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_ATLAS_COLORS and default atlas in AFNI GUI
Set atlas to use for Atlas colors, Go to atlas location,
Draw Dataset and Renderer. Name of atlas can be set in
environment and modified in the AFNI GUI environmentalism menu.
Several other environmental variables regarding atlas usage
can also be modified there too.
08 Jul 2011, RW Cox, AFNI, level 1 (MICRO), type 4 (BUG_FIX)
Tips HTML window crashes on kampos (Solaris)
Debugging shows XmHTML crashed when rendering different-than-normal
fonts. Solution = strip font-changing HTML tags out of file before
display -- only on systems marked as evil in this way.
08 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 5 (MODIFY)
added -on_surface, which might not end up being so useful
06 Jul 2011, RC Reynolds, uber_align_test.py, level 1 (MICRO), type 5 (MODIFY)
test use of SUBJ.set_var_with_defs
06 Jul 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 0 (GENERAL)
create anat_final dset, as one that is aligned with the stats
Also, suggest use of uber_subject.py in the -ask_me dialog.
05 Jul 2011, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
add -NOLINE to include clipping of points outside the box
05 Jul 2011, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
minor enhancements to 5 python files (prep for gen_ss_review_scripts.py)
01 Jul 2011, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
Replace text-only AFNI Tips with HTML-based
Allows incorporation of images and better formatting.
Uses XmHTML widget set, whose source code is also added to AFNI.
30 Jun 2011, RC Reynolds, afni_proc.c, level 1 (MICRO), type 5 (MODIFY)
renamed aligned anat output (from align_epi_anat.py)
This should make it clear whether or not the output anat should be used
28 Jun 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 3 (NEW_ENV)
Ability to skip the 'centering' done in AM2 regression
By setting environment variable AFNI_3dDeconvolve_rawAM2 to YES, as in
the command
3dDeconvolve -DAFNI_3dDeconvolve_rawAM2=YES ...
27 Jun 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Add README.afnigui and AFNI Tips button
27 Jun 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT)
added -dset_index0_list/-dset_index1_list options, etc.
- ttest++ and MEMA commands now apply directories to datasets
- changed Subject.atrs to be VarsObject instance, not dictionary
27 Jun 2011, RC Reynolds, thd_table.c, level 1 (MICRO), type 5 (MODIFY)
output warning hint on single column covariate file
27 Jun 2011, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
changed decode_1D_ints to take imax param
Affects 1d_tool.py, xmat_tool.py and any utilities using lib_afni1D.py.
Also added restrict_by_index_lists().
27 Jun 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_WHEREAMI_DEC_PLACES
Set precision for whereami output
Higher field data and animal atlases require higher precision.
The default value used for focus point among template spaces is
still 0 decimal places (closest mm), but animal data requires three
decimal places. Value may range from 0 to 10.
24 Jun 2011, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT)
added global option -pif which is used to flag certain commands.
-pif PROCESS_ID_FLAG is used to flag a particular AFNI command
so that you can identify from the shell that command's process id
by grepping for PROCESS_ID_FLAG on the output of 'ps -a'.
24 Jun 2011, RC Reynolds, slow_surf_clustsim.py, level 3 (MAJOR), type 1 (NEW_PROG)
a temporary program until we do this in C
23 Jun 2011, RW Cox, afni InstaCorr, level 2 (MINOR), type 5 (MODIFY)
Ability to INIT-ialize InstaCorr from a plugout
Details are in README.driver, under the INSTACORR command section.
23 Jun 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
Desai MPM atlases
New maximum probability map atlases derived from the Desai probability
maps just introduced in distribution.
20 Jun 2011, ZS Saad, @ROI_Corr_Mat, level 1 (MICRO), type 4 (BUG_FIX)
added support for +tlrc input, more debugging messages, -echo option.
20 Jun 2011, ZS Saad, 3drename, level 1 (MICRO), type 2 (NEW_OPT)
added support for -overwrite
20 Jun 2011, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
added eta2 function (alongside '3ddot -doeta2')
17 Jun 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Button3 (right) click image viewer 'Disp' to raise AFNI controller
17 Jun 2011, RC Reynolds, SUMA_MiscFunc.c, level 1 (MICRO), type 4 (BUG_FIX)
set 0-length BmP array to matching length 3
16 Jun 2011, ZS Saad, 3dSurfMask, level 3 (MAJOR), type 2 (NEW_OPT)
Major improvements for mask creation and voxel distance computations
Option -fill_method SLOW produces more accurate masks for voxels
inside the closed surface. In addition, the program outputs a dataset
with the shortest distance of each voxel to the surface.
See examples under 3dSurfMask -help.
16 Jun 2011, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
-flip_orientation allows for reversing triangle orientation.
See new examples under SurfPatch -help
16 Jun 2011, ZS Saad, SurfPatch, level 2 (MINOR), type 4 (BUG_FIX)
No longer complains about not finding seed in cases where it should.
16 Jun 2011, RC Reynolds, 3ddot, level 2 (MINOR), type 2 (NEW_OPT)
added -doeta2 via new THD_eta_squared_masked
Added for Shinchan.
16 Jun 2011, RC Reynolds, 3dAutoTcorrelate, level 1 (MICRO), type 4 (BUG_FIX)
allowed very small datasets
15 Jun 2011, RW Cox, 3dmaskave, level 1 (MICRO), type 2 (NEW_OPT)
Add -sum option; rearrange -help output a little.
15 Jun 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 6 (ENHANCE)
if constant dset names, extract SIDs from dir names
Done for R Momenan.
10 Jun 2011, DR Glen, whereami, level 4 (SUPER), type 0 (GENERAL)
Generic Atlas Support and new atlases
Atlases, spaces and transformations are now defined in a NIML file,
AFNI_atlas_spaces.niml. Transformations among spaces for coordinates
are defined in that file for use by whereami and the whereami display
in the AFNI GUI. The flexible naming of the spaces and atlases allows
easy addition of new atlases to AFNI processing.
Two new environment variables control what atlases and spaces are shown
when no atlas is specified, AFNI_ATLAS_LIST and AFNI_TEMPLATE_SPACE_LIST
The list of atlases now defaults to the TT_Daemon and the Eickhoff-
Zilles atlases in MNI_ANAT space.
Additionally, the cytoarchitectonic atlases from the Zilles, Eickhoff
group have been updated to the most recent version, 1.8.
***The previous versions, 1.5, are not used in this release by default.
Depending upon differences on how regions or codes are defined and used,
it is possible that processing scripts and results may be affected.
With this release, we also introduce three probabilistic atlases
donated by the Desai group generated from a typical AFNI pipeline.
These atlases contain a multitude of regions created using both
@auto_tlrc and FreeSurfer.
08 Jun 2011, ZS Saad, afni-general, level 3 (MAJOR), type 2 (NEW_OPT)
Added -npb and modified title bar to reflect bloc of ports
You can have multiple instances of programs talking to each other.
See afni's help for details on the -npb option.
08 Jun 2011, ZS Saad, @FSlabel2dset, level 2 (MINOR), type 1 (NEW_PROG)
Script to change FreeSurfer ascii label file to SUMA dset
08 Jun 2011, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed print and added min_rest to durations in test of -tr_locked
07 Jun 2011, ZS Saad, afni-general, level 3 (MAJOR), type 2 (NEW_OPT)
Allow multiple instances of communicating programs per machine.
This was done by generalizing option -np PORT_OFFSET which
allows users to use a different set of ports for different AFNI/SUMA/etc.
sessions.Port numbers should no longer be hard coded anywhere. New dedicat
ed
ports should be added to then new init_ports_list() function.
07 Jun 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added 'w' key for writing out colormap to disk.
See suma's help for the colormap.
(press ctrl+h with cursor over the colormap in the surface controller)
07 Jun 2011, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT)
-np, -list_ports, -port_number* control and report port assignments
See suma -help for details.
07 Jun 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT)
-list_ports, -port_number* give port assignment information
See afni -help for details.
07 Jun 2011, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
modify number of points used for optimization
Powell's NEWUOA algorithm requires specifying number of points kept at
each stage for approximating the objective function. Modification here
is to change this number as the various steps of registration happen,
using fewer points at the start and more at the final steps. Speeds
things up a little.
06 Jun 2011, RW Cox, powell_newuoa.c, level 1 (MICRO), type 0 (GENERAL)
Remove 'static' and initialize all variables to 0.
Makes tiny differences in 3dAllineate results. Hmmm.
03 Jun 2011, RC Reynolds, Makefile, level 2 (MINOR), type 2 (NEW_OPT)
removed -lpng from Makefile.macosx_10.6_Intel_64
We added -lpng because we were compiling our own OpenMotif
(configure option?), but fink's version does not need it.
03 Jun 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT)
added -volreg_compute_tsnr/-regress_compute_tsnr
Volreg TSNR is no longer the default, but regress TSNR is.
02 Jun 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
compute TSNR datasets (added -compute_tsnr); added -regress_make_cbucket
02 Jun 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
de-meaned motion regressors is now the default
- added -regress_apply_mot_types to specify motion types for regression
- added -regress_no_motion_demean and -regress_no_motion_deriv
- by default, demean and deriv motion parameters are created
- by default, demean motion parameters are applied in the regression
(replacing the original 'basic' parameters, which should have no
change in betas of interest, just the constant polort betas)
31 May 2011, RW Cox, data loading, level 1 (MICRO), type 0 (GENERAL)
Allow mmap for supra-2GB .BRIK files
Change DBLK_mmapfix macro (3ddata.h) to work for larger files on 64-bit
systems -- with sizeof(size_t) == 8. Also print an informative message
in thd_loaddblk.c when mmap-ing more than 1GB.
27 May 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
re-work of motion, as prep for more motion options
- replaced -volreg_regress_per_run with -regress_motion_per_run
- made uniq_list_as_dsets() a warning, not an error (for J Britton)
27 May 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -split_into_pad_runs (for regress motion per run)
26 May 2011, RW Cox, thd_cliplevel, level 1 (MICRO), type 4 (BUG_FIX)
Problem with overflow when image has tiny float values
This affects a bunch of programs, including any program that has
automasking. In the computation of the cliplevel of a float dataset,
the dataset is scaled to shorts for histogram-ization, and that scaling
is computed as 10000/maxval -- but if maxval is very tiny (say 1e-35),
then the scale factor is float overflow -- which doesn't work so well
farther on. The solution is to compute the scale factor in double
precision. Or to have less silly users.
26 May 2011, RW Cox, mri_read, level 1 (MICRO), type 5 (MODIFY)
Add warning message for ANALYZE scale factors too big or too small
26 May 2011, RW Cox, All, level 1 (MICRO), type 0 (GENERAL)
new AFNI version as of today
Just because -- it's been 7 months.
25 May 2011, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
Fix problem with TENT and CSPLIN
For non-integer TR, could miss evaluating the last function in a TENT or
CSPLIN series because of roundoff error pushing the evaluation time
slightly past the 'top' value. This is bad if the function is 1 at
exactly this value, as the last functions are here. Solution was to
change the test to allow evaluation at values slightly larger than
'top'.
25 May 2011, RW Cox, thd_zzprintf, level 1 (MICRO), type 4 (BUG_FIX)
Patched to avoid string overruns for crazy users
25 May 2011, RW Cox, @1dDiffMag, level 1 (MICRO), type 1 (NEW_PROG)
Computes magnitude of 1st differences of 1D file
25 May 2011, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT)
Add -tdiff option == statistics on first differences of data
25 May 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -global_to_local and -local_to_global for G Chen
24 May 2011, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
Add -noline and -box options
To plot markers at each point, without or with lines connecting them.
24 May 2011, RC Reynolds, 1dplot, level 2 (MINOR), type 4 (BUG_FIX)
fixed plotting of varying length time series
20 May 2011, RW Cox, 1dCorrelate, level 2 (MINOR), type 2 (NEW_OPT)
Add normal theory CI for Pearson; Add -block option
Pearson correlation (the default) now gets the normal theory confidence
interval printed at no extra charge.
To allow for serial correlation, the -block option enables random length
block resampling bootstrap.
Add some more help text to explicate things a little better.
20 May 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 5 (MODIFY)
execute via /usr/bin/env python
Help now suggests fink as primary Mac source for PyQt4.
20 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 5 (MODIFY)
execute via /usr/bin/env python
19 May 2011, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT)
Added support for multiple reference time series.
Search for -var* options in @RetinoProc -help.
19 May 2011, ZS Saad, 3dRetinoPhase, level 2 (MINOR), type 2 (NEW_OPT)
Added option to use best of multiple reference time series.
Search for -multi_ref_ts in 3dRetinoPhase -help
19 May 2011, RW Cox, 1dCorrelate, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation coefficients of 1D columns
Pearson, Spearman, Quadrant, or Kendall tau_b.
Main goal is to provide the bias-corrected bootstrap estimate of the 95%
confidence interval.
18 May 2011, ZS Saad, @RetinoProc, level 3 (MAJOR), type 2 (NEW_OPT)
Added options for mapping to specific layers, and the use of delay
The options -wm, -pial, etc. allow for tight control of mapping
onto specific layers in the cortex.
Option -delay improves latency estimation compare to using the phase
of the fundamental frequency.
18 May 2011, ZS Saad, 3dRetinoPhase, level 3 (MAJOR), type 2 (NEW_OPT)
Added options to 3dRetinoPhase to estimate latency as in 3ddelay
The two options for computing delays, instead of phase, are
-phase_estimate DELAY, and -ref_ts REF_TS . See program's -help for
details.
Also added -ort_adjust which is needed to account for lost DOF in
external detrending when estimating the significance of correlation
coefficients with delay estimation.
The program now output a correlation coefficient with the visual field
angles datasets.
And speaking of correlation coefficients, the significance levels should
be taken with a grain of salt, especially in derived datasets such as
field angle, and VFR in SurfRetinoMap.
18 May 2011, ZS Saad, SurfRetinoMap, level 2 (MINOR), type 5 (MODIFY)
Added a correlation coefficient with VFR output.
18 May 2011, ZS Saad, 3ddelay, level 2 (MINOR), type 2 (NEW_OPT)
Added options to 3ddelay to improve its utility for retinotopy analysis
The new options are -phzreverse and -phzscale. Though useful, you are
better off using 3dRetinoPhase -phase_estimate DELAY option. It is much
more convenient for retinotopy analysis and fits better in @RetinoProc
18 May 2011, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Node value now updates when switching dsets while viewing surf patches.
16 May 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Make 'Points' display in grapher get bigger with thicker lines
Otherwise, thick lines hide the points. Done via XFillArc function.
16 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 6 (ENHANCE)
could be used as a release version
- added 'check center dist' button, to display the current distance
- added menu item to show afni command for viewing results
- added menu items to show python and shell command windows
- added much more help, including main and section buttons
- added browsing of align_epi_anat.py help
16 May 2011, RC Reynolds, afni_util.py, level 1 (MICRO), type 6 (ENHANCE)
added exec_tcsh_command function
16 May 2011, RC Reynolds, @Center_Distance, level 1 (MICRO), type 6 (ENHANCE)
return something to $status, so we can detect success or failure
13 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 6 (ENHANCE)
added working GUI (for options, GUI help still needs ... help)
12 May 2011, RC Reynolds, uber_skel.py, level 3 (MAJOR), type 1 (NEW_PROG)
A working skeleton for future uber programs.
This is based on uber_align_test.py, version 0.2.
12 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 6 (ENHANCE)
many small updates
This set of 3 files was broken off set uber_skel.py, meant to be a
resonable starting point for future uber programs.
auto-generated by afni_history on May 10 2013