AFNI HISTORY
level 2 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 2 -past_years 2
---- log of AFNI updates (most recent first) ----
24 Nov 2009, ZS Saad, afni-matlab, level 2 (MINOR), type 4 (BUG_FIX)
Stopped writing empty attributes which caused trouble in AFNI.
Empty attributes make AFNI halt the parsing of the header.
23 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Workaround for connection drop between AFNI and SUMA in Shared Memory Mode.
Env SUMA_AttemptTalkRecover allows SUMA to recover from drop.
This ENV is set by default to No.
23 Nov 2009, G Chen, 3dKS.R, level 2 (MINOR), type 1 (NEW_PROG)
Kolmogorov-Smirnov test
This is an R program that runs Kolmogrov-Smirnov test between
two groups of subjects. It takes individual sub-brick files from
each subject as input and spills two sub-bricks in the output,
first one being the Kolmogorov-Smirnov statistic D, while the 2nd
the corresponding Z-score.
20 Nov 2009, DR Glen, 3dAutomask, level 2 (MINOR), type 2 (NEW_OPT)
apply_prefix option to save automasked input
avoids 3dcalc step that is usually used to apply an automask.
19 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed recorder lag on OS X machines.
On OS X platforms, the 'r' or 'R' recording modes
used to record the previous image it seems.
17 Nov 2009, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
SUMA now handles labeled datatets in a special manner
An example of a labeled dataset would be FreeSurfer's annotation files.
If an annotation file is present in the spec file (@SUMA_Make_Spec_FS),
SUMA will display it as part of the background.
You can chose to display the labeled dataset in color, contours, or both.
Data from labeled datasets is now shown under the 'Lbl' field in the
surface controller's Xhair block.
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_AlwaysAssignSurface (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_LabelDsetOpacity (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ConvexityDsetOpacity (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ShowLabelDsetAtStartup (see suma -environment for details)
17 Nov 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT)
Option -label_dset creates a labeled dataset from ROIs.
Labeled datasets are now rendered in a special manner in SUMA
17 Nov 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
Option -dset creates a labeled dataset from annotation file.
Labeled datasets are now rendered in a special manner in SUMA
17 Nov 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Script now automatically sets up the spec file with labeled datasets
Labeled datasets are created from annotation files,
and are now rendered in a special manner in SUMA
16 Nov 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
allow motion censoring with varying run lengths
Also, if a max is applied in scaling, explicitly limit to [0,max].
16 Nov 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY)
allow motion censoring with varying run lengths
09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added options to check for, and correct 'bowties' in pathches.
Bowties in patches result in non 2-manifold stiched surfaces whose
volume cannot be caluclated. The *bowtie option deal with such cases.
09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added options to shrink patch contours at nodes not in selected nodes.
See options -adjust_contour for details.
09 Nov 2009, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT)
Added option for improved node volume estimation.
The new measure, called node_volg, uses Gauss' Theorem to estimate
the volume associated with a node in two isotopic surfaces. This option
is more robust to surface curvature variations.
04 Nov 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
3dAllineate option for motion correction
volreg_method allows 3dAllineate, which is useful for DTI data.
Bug fix for post-transformation matrix and dataset view
27 Oct 2009, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added support for optional LabelTable RGBA attributes
23 Oct 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -censor_fill and -censor_fill_par
These options are to zero-pad TRs that were censored by 3dDeconvolve.
19 Oct 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options for using 3dBlurInMask, instead of 3dmerge
- added -blur_in_mask, -blur_in_automask and -blur_opts_BIM
- added -sep_char and -subj_curly
19 Oct 2009, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 2 (NEW_OPT)
New master options, dset1/2 terminology
New master_nnn_dxyz options to specify output resolution
dset1 and dset2 for non-EPI/anat alignment with lpa cost function
and turns off preprocessing steps
giant_move option turns off resampling and changes master options
Expanded help - including fuller description of edge method
Removed volume registration (motion correction) for anat2epi option
by default.
AFNI dataset views (+orig/+acpc/+tlrc) are maintained in output
depending on BASE, SOURCE or external dataset names for all output
14 Oct 2009, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Direct viewing of pre-processed datasets in Dot xform
14 Oct 2009, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
New help window for Dot xform
07 Oct 2009, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT)
Add -Mmask option to allow multiple mask values
For independent blurring (e.g., blur WM and GM separately).
06 Oct 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
More bug fixes related to ROI loading, and OSX's GLX problem
29 Sep 2009, RW Cox, afni, level 3 (MAJOR), type 5 (MODIFY)
InstaCalc is more-or-less ready
At least, I let Mike Beauchamp test it for his cunning plans.
29 Sep 2009, RC Reynolds, @Reorder, level 2 (MINOR), type 1 (NEW_PROG)
script version of reorder plugin, for J. Bjork
29 Sep 2009, DR Glen, RetroTS, level 2 (MINOR), type 2 (NEW_OPT)
Flexible slice timing options
SliceOrder option allows for standard slice timing order
alt+z, alt-z, seq+z, seq-z, Custom and 1D text file input
29 Sep 2009, DR Glen, McRetroTS, level 2 (MINOR), type 2 (NEW_OPT)
Opt options available to compiled version
All options available through the Opt structure are now available
even with the compiled version of McRetroTS, making the compiled version
functionally equivalent to the RetroTS.m version
24 Sep 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed crashes on OS X 10.5 caused by OS X's buggy GLX implementation
24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Improved the 'star' blurring interface.
24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Setup final color blurring level.
18 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Added option -n minnodes
18 Sep 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
Allow specifying external FreeSurfer color table.
16 Sep 2009, RC Reynolds, 3ddot, level 2 (MINOR), type 4 (BUG_FIX)
de-meaning data causes permission-based seg fault, apply means upon read
Found by Giuseppe Pagnoni.
14 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Allow specifying rmm in number of edges connecting nodes.
09 Sep 2009, ZS Saad, @fast_roi, level 2 (MINOR), type 2 (NEW_OPT)
Allow @fast_roi to accept existing TLRC transformed anatomy
09 Sep 2009, RW Cox, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
Add 'ball' options for mask generation
08 Sep 2009, DR Glen, whereami, level 2 (MINOR), type 5 (MODIFY)
Allows MNI_ANAT space for whereami
Subtracts 8mm I-S and uses MNI space transform to TTA
08 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Properly allows post-transformation matrix
04 Sep 2009, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
registration can now be consistent across runs
Reg Base can be 'Current': to set the base volume from the current run
(call this the old way), 'Current & Keep': use current run, but then
store that base and apply it to future runs, 'External Dataset': fix the
base from some chosen dataset.
Using 'Current & Keep' makes sense for realtime registration.
03 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixes for certain combinations
Allowed BASE and SOURCE specification for oblique data
Allowed 3dWarpDrive volume registration with mean/max base
Removed anatomical output with oblique data and only epi2anat
26 Aug 2009, RW Cox, 3dFFT, level 2 (MINOR), type 1 (NEW_PROG)
Compute spatial 3D FFT of a dataset
* This is for John Butman
* Was started a long time ago, but only finished today
* Probably useless
25 Aug 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Provide keystroke fine control over cropping in image viewer
Shift+arrowkey = scroll crop window
Ctrl+arrowkey = resize crop window
Right-click on crop button = menu to set size exactly
Hint on crop button = shows crop parameters
25 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
if volreg block, always create motion_${subj}_enorm.1D
21 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_censor_motion and -regress_censor_prev
Motivated by L Thomas and B Bones.
20 Aug 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added motion censoring options
Added -censor_motion, -censor_prev_TR, -collapse_cols, -extreme_mask,
-set_tr, -write_censor and -write_CENSORTR.
Also modified afni_util.py, lib_afni1D.py and option_list.py.
14 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -align_epi_ext_dset, to align anat to external EPI
This may be important for multi-channel coil EPI data with low internal
structural contrast. Users might align to the first (pre-steady-state)
TR, even though that volume is not used in the analysis.
13 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -volreg_tlrc_adwarp, to apply a manual Talairach transformation
10 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
truncate min dim to 3 sig bits for -volreg_tlrc_warp/-volreg_align_e2s
The old default was 2 bits, -volreg_warp_dxyz overrides.
10 Aug 2009, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 5 (MODIFY)
allow processing of -overwrite and AFNI_DECONFLICT
06 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed problems found by I Mukai and K Bahadur
- fixed -volreg_align_to base as applied in align_epi_anat.py
- fixed blur 'averages' computation when only one run
04 Aug 2009, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT)
added basic demo interface and itemized exception traps
29 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed creation of extents mask when only 1 run
28 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 5 (MODIFY)
if known, require proper slice regressor ordering in -slibase* opts
27 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
use -slibase_sm instead of -slibase in 3dREMLfit
27 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -slibase_sm, for slice-major ordering of regressors
RetroTS and afni_proc.py were incorrectly using this ordering.
** Analysis done prior to this probably needs to be re-done.
27 Jul 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_labels and -show_label_ordering
23 Jul 2009, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -partition option
23 Jul 2009, RC Reynolds, afni_run_R, level 2 (MINOR), type 5 (MODIFY)
allow any number of args, but where first is program, last is output
23 Jul 2009, DR Glen, MEMRI models, level 2 (MINOR), type 2 (NEW_OPT)
Single and Dual exponential models
New models for 3dNLfim that use single and dual exponential models
that are appropriate for MEMRI (Manganese Enhanced MRI
22 Jul 2009, RC Reynolds, realtime_reaceiver.py, level 3 (MAJOR), type 1 (NEW_PROG)
python replacement for serial helper
New 'data_choice' options can be added to compute_data_for_serial_port
for sending results of a different computation to the serial port.
21 Jul 2009, RW Cox, niml_feedme, level 2 (MINOR), type 1 (NEW_PROG)
Test and demo program showing how to set datasets to AFNI via NIML
An analog to rtfeedme. Sends volumes to AFNI using VOLUME_DATA
elements. Pretty rudimentary.
21 Jul 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Update widgets and viewing when VOLUME_DATA is added to a dataset
* Fix AFNI_setup_viewing() to update widgets properly when dataset nvals
changes
* Add function AFNI_update_dataset_viewing() to deal with viewing
changes that might be needed if a dataset is altered
16 Jul 2009, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added option to force autoscale on the graphing window
The option is accessible by pressing 'A' in the graph window
or under 'Graph->Opt->Scale->AUTO'.
16 Jul 2009, RC Reynolds, realtime_receiver.py, level 3 (MAJOR), type 1 (NEW_PROG)
replacement for serial_helper
14 Jul 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -max_rest, to limit the maximum duration of rest periods
14 Jul 2009, DR Glen, afni, level 2 (MINOR), type 3 (NEW_ENV)
Added AFNI_ONE_OBLIQUE_WARNING
AFNI_ONE_OBLIQUE_WARNING = YES makes interactive spit out ONE warning
about obliquity per session then go quiet.
13 Jul 2009, RW Cox, 3dLocalstat, level 2 (MINOR), type 5 (MODIFY)
OpenMP
Also added option '-use_nonmask' to allow statistics to be computed for
voxels not in the mask (but presumably whose neighbors are in the mask).
25 Jun 2009, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
fixed dz sent to RT plugin for oblique datasets
24 Jun 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 0 (GENERAL)
Modify to use OpenMP more effectively.
Have to avoid use of Doug's matrix.c functions in the main loops, since
they do so much malloc/free, which blocks other threads from running.
Instead, rewrote versions of the needed functions that use pre-allocated
workspace arrays. Speedup is very good now for the REML setup and REML
voxel loops. Haven't decided whether to OpenMP-ize the GLSQ or OLSQ
loops, since these usually take much less time.
24 Jun 2009, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
applied print changes from B Feige (26 files):
3dfim.c afni.c afni_niml.c mri_free.c mrilib.h 3dmatmult.c NLfit_model.c
suma_datasets.h gifti/gifti_tool.c rickr/serial_helper.c
SUMA/ SUMA_3dSurfMask.c SUMA_ConvertSurface.c SUMA_CreateIcosahedron.c
SUMA_Load_Surface_Object.c SUMA_MapIcosahedron.c SUMA_NikoMap.c
SUMA_ParseCommands.h SUMA_SphericalMapping.c
SUMA_Surf2VolCoord_demo.c SUMA_Surface_IO.c SUMA_SurfWarp.c
SUMA_compare_surfaces.c SUMA_xColBar.c
svm/3dsvm.c svm/3dsvm_common.c volpack/vp_octree.c
23 Jun 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX)
added 4 checks of alloc() returns
17 Jun 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
version 2.0 : call e2a alignment and warp to standard space ready
- mask warped EPI by its extents (at volreg step)
- added -volreg_no_extent_mask, to block this masking
- added 'extents' to list of mask in -mask_apply
- change block dividers to more visual '===' with block names
17 Jun 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -make_3dd_contrasts and used general accuracy in block durations
17 Jun 2009, DR Glen, RetroTS.m, level 2 (MINOR), type 4 (BUG_FIX)
Number of TRs found incorrectly because of rounding
17 Jun 2009, DR Glen, McRetroTS.m, level 2 (MINOR), type 1 (NEW_PROG)
Matlab Compilable version of RetroTS.m
This version calls the RetroTS function, but can be compiled
for users that either do not have Matlab, a required toolbox
or want to use this function in a shell script more easily.
15 Jun 2009, RC Reynolds, 3dmerge, level 2 (MINOR), type 5 (MODIFY)
allowed short/byte datasets to use FIR blur, so no Fourier interpolation
Also added Y/N AFNI_BLUR_INTS_AS_OLD env var to use previous method.
15 Jun 2009, DR Glen, BrikLoad.m, level 2 (MINOR), type 4 (BUG_FIX)
Typo in BrikLoad
Gremlin got to Pixy
11 Jun 2009, RW Cox, AlphaSim, level 2 (MINOR), type 5 (MODIFY)
Added computation of analytic approximation of Alpha(i) for large i
Uses a modified extreme value distribution, which looks pretty good.
11 Jun 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added masking abilities
- in mask block, try to create anat and group masks
- added -mask_apply option, for choosing mask to apply to regression
- added -align_opts_aea, for extra opts to align_epi_anat.py
29 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -execute and now fail if block options have no corresponding blocks
28 May 2009, RC Reynolds, strblast, level 2 (MINOR), type 4 (BUG_FIX)
partial words had resulted in skipping ahead
found by R Notestine of UCSD
28 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
example updates for AFNI_data4 and new options
27 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
updates for alignment/warp/varying run lengths
- added -volreg_warp_dxyz option
- if align a2e, add -no_ss to @auto_tlrc
- for varying run lengths, fixed application of '-volreg_align_to last'
and the -regress_est_blur_* options
(blur estimation loops were modified for this)
- warping to new grid truncates to 2 significant bits (if < 2 mm)
22 May 2009, ZS Saad, @FS_roi_label, level 2 (MINOR), type 1 (NEW_PROG)
A script to get FreeSurfer parcellation and annotation labels
The script is used to return a label associated with a FreeSurfer
annotation or parcellation integer label.
21 May 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Additional check for caret-version string
It seems that the syntax for caret-version has changed
slightly and was being missed by SUMA. As a result, Caret
surfaces were not being properly aligned with the volumes.
21 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added 'align' processing block and -volreg_align_e2a option
20 May 2009, RW Cox, realtime plugin, level 2 (MINOR), type 5 (MODIFY)
Modified to allow realtime 3D registration on complex inputs
Mostly a change in mri_3dalign.c, to take the movement estimation done
on the magnitude image and apply it to the 2 component images.
20 May 2009, G Chen, 3dMEMA.R, level 4 (SUPER), type 1 (NEW_PROG)
Mixed-Effects Meta Analysis (MEMA)
This is an R program that runs group analysis in a truly random
mixed-effects sense by taking both beta and t-statistic as input
instead of beta value only in the conventional method. See more
details at http://afni.nimh.nih.gov/sscc/gangc/MEMA.html
19 May 2009, ZS Saad, @ROI_Corr_Mat, level 3 (MAJOR), type 1 (NEW_PROG)
A script to calculate correlation matrices between ROI time series
Calculates the correlation matrices between average time series from ROIs
defined in a mask volume. Script was written with Hang Joon Jo.
19 May 2009, ZS Saad, prompt_user, level 2 (MINOR), type 1 (NEW_PROG)
Prompts user for input with an X window
19 May 2009, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
Added -zerofill and -roisel options
Added options to force output for empty ROIs.
19 May 2009, ZS Saad, 1ddot, level 2 (MINOR), type 2 (NEW_OPT)
Added -okzero to keep program from exiting with all zero input
Added options to force output for empty ROIs.
15 May 2009, RW Cox, afni InstaCorr, level 2 (MINOR), type 0 (GENERAL)
Remove OpenMP; carry out setref on all locked controllers
15 May 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
added -volreg_tlrc_warp option: can warp to standard space at volreg step
13 May 2009, RW Cox, InstaCorr+3dBlurInMask, level 2 (MINOR), type 0 (GENERAL)
Added OpenMP support for blurring to these programs
Parallelization occurs across sub-bricks -- speedup is significant.
11 May 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
InstaCorr changes
* Save seed time series into the 1D timeseries library for graphicking
* Modify progress printouts slightly
08 May 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Better display of ROI contours on patches
Suma now correctly handles ROI display when the ROIs
contain nodes that are not in the patch. Also, on flat surfaces,
ROI contours are drawn raised so that they float over flat surfaces.
08 May 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
The script now automatically turns FS annot files to SUMA ROI files
08 May 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Instacorr updates
* Can Write A_ICOR datasets using new allow_directwrite variable
* Disable InstaCorr when switching sessions and views
* Notify renderer (DRAWNOTICE) when changes made
* Shift-Ctrl-Left-Click does crosshair shift + InstaCorr Set
07 May 2009, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
FIxes/upgrades for InstaCorr
* memory problem fixed by malloc-ing sizeof(float *)
-- not sizeof(float) -- for a float ** variable!
* add dataset labels
* add statistical parameters (including FDR)
* add help
06 May 2009, RW Cox, afni, level 3 (MAJOR), type 2 (NEW_OPT)
First edition of InstaCorr!
Rough around the edges, but gnarly-ific to the level of the first
inaccessible cardinal!
05 May 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 4 (BUG_FIX)
Added 'd' and 'j' keys
05 May 2009, ZS Saad, 3dRank, level 2 (MINOR), type 1 (NEW_PROG)
A program that substitutes a voxel's value by that value's rank
05 May 2009, RC Reynolds, plug_render, level 2 (MINOR), type 5 (MODIFY)
now built from plug_null.c, so it will no longer be available
05 May 2009, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 1 (NEW_PROG)
another script to update the AFNI package
01 May 2009, RW Cox, 3dBlurInMask, level 2 (MINOR), type 1 (NEW_PROG)
Like 3dBlurToFWHM, but simpler.
01 May 2009, DR Glen, 1dSEM, level 2 (MINOR), type 4 (BUG_FIX)
Tree growth fix
Fixed bug in tree growth and improved output text
30 Apr 2009, RC Reynolds, vol2surf, level 2 (MINOR), type 2 (NEW_OPT)
return a node v2s time series when afni changes xhair position
30 Apr 2009, RC Reynolds, thd_niftiread, level 2 (MINOR), type 5 (MODIFY)
be sure to warn users when nifti is converted to float (w/dglen)
30 Apr 2009, RC Reynolds, 3dcalc, level 2 (MINOR), type 5 (MODIFY)
changed atan2(y,x) to proceed if y OR x is non-zero
29 Apr 2009, ZS Saad, SurfSmooth, level 2 (MINOR), type 4 (BUG_FIX)
-detprefix_* options now do something!
29 Apr 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT)
-nodelist* options to output node sequence forming ROI
29 Apr 2009, ZS Saad, MapIcosahedron, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash when using -it option for geometry smoothing
29 Apr 2009, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT)
-node_select_1D now respects node ordering
29 Apr 2009, ZS Saad, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT)
-VarThresh* options for obtaining counts at different thresholds
29 Apr 2009, RW Cox, afni, level 2 (MINOR), type 3 (NEW_ENV)
Make 'Where am I?' font size user controllable.
via AFNI_TTATLAS_FONTSIZE environment variable (editable).
29 Apr 2009, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
when opening -geomparent, allow for known non-afni extensions
28 Apr 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Add duration argument to SPMGx basis functions for deconvolution.
For Tracy Doty, apparently.
28 Apr 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 5 (MODIFY)
uppercase file extensions are now valid
23 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
updates to help and tcsh options
- added -f as a recommended tcsh option
- added help section 'SCRIPT EXECUTION NOTE'
- reordered help: intro, BLOCKS, DEFAULTS, EXAMPLES, NOTEs, OPTIONS
- shifted execution command to separate line
22 Apr 2009, DR Glen, @AddEdge, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Oblique edge display
Fixed bug with oblique data in edge display
16 Apr 2009, RW Cox, All, level 2 (MINOR), type 4 (BUG_FIX)
Inadvertent recursion in afni_environ.c now blocked.
14 Apr 2009, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
niml ROI files with empty ROI no longer crash suma/ROI2dataset
14 Apr 2009, RC Reynolds, NIfTI, level 2 (MINOR), type 2 (NEW_OPT)
added sample nifticlib program: clib_01_read_write.c
11 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -volreg_regress_per_run
This is to apply the motion parameters of each run as separate regressors.
11 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -derivative and -set_nruns, fixed -show_cormat_warnings typo
10 Apr 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Error in processing -slibase file with censoring
Typo in replacing input image with censored image caused the end of the
world (SEGV crash).
10 Apr 2009, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT)
added -use_last_elem option for setting DICOM elements
Can also use AFNI_DICOM_USE_LAST_ELEMENT environment variable.
10 Apr 2009, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -use_last_elem option for setting DICOM elements
10 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY)
fix for old versions of python, like on solaris
Each of copy.deepcopy(), sum(), and sort(reverse=True) failed.
09 Apr 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
'official' release with RETROICOR processing block: ricor
o added 'across-runs' ricor_regress_method
o added ricor information and usage to help (see 'RETROICOR NOTE')
o maintain unscaled shorts if they are input
o added -ricor_datum
09 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_cormat_warnings and -cormat_cutoff
08 Apr 2009, RW Cox, thd_filestuff.c, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_ALLOW_ARBITRARY_FILENAMES
Set this environment variable to YES to allow 'strange' characters into
AFNI created filenames. You should know what you are doing if you use
this variable!
08 Apr 2009, RW Cox, AFNI image viewer, level 2 (MINOR), type 5 (MODIFY)
Set MPEG 'pattern' for frames to reflect the Anim_dup setting.
This small change will make MPEG-1 (.mpg) files that are slowed down by
setting Anim_dup > 1 not significantly larger than full speed files, by
setting the frame pattern to 'IPPPP' where the number of Ps is the
number of duplicate frames (Anim_dup-1).
08 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_rows_cols option
06 Apr 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added support for '.', ',', and space keys, and 'shw_0'
04 Apr 2009, RW Cox, 3dmaskSVD, level 2 (MINOR), type 1 (NEW_PROG)
Like 3dmaskave, but does SVD principal vector instead of average
02 Apr 2009, RW Cox, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT)
Add -Thresh option
To save a count of how many other voxels are above threshold correlated
with each seed voxel.
02 Apr 2009, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
changed CHECK_NIFTI to CHECK_NEEDS_FLOATS, including other dset types
01 Apr 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Arrow keys based navigation along surface.
See 'Alt+U-D' section in SUMA's interactive usage help.
01 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
added 'ricor' processing block, for RETROICOR regressor removal
31 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Handling of double precision datatypes.
31 Mar 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added 'on the fly' dot product computation
This feature is only available with SUMA's -dev
option. It is still in testing mode and its
interface may change. If intrigued, see 'D' key's
help in SUMA's interactive usage help.
31 Mar 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added support for '[' and ']' keys and -view_surf
31 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
small changes, and prep for retroicor
- by default, the script will now terminate on any error
- added -exit_on_error, -check_setup_errors
- whine about block order problems
31 Mar 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -pad_to_many_runs, -reverse
30 Mar 2009, RW Cox, 3dABoverlap, level 2 (MINOR), type 1 (NEW_PROG)
Computes various overlap and non-overlap statistics for 2 datasets.
Will resample dataset #B to match dataset #A, if needed. This program
is intended to check if two datasets are grossly not aligned, and has
little other purpose.
27 Mar 2009, RW Cox, FDR calculations, level 2 (MINOR), type 5 (MODIFY)
Changes/additions to mask operations for FDR curves.
3dREMLfit and 3dDeconvolve now generate an automask for the FDR curving
purposes, if no other mask is used. 3drefit has a new -FDRmask option
for computing the FDR curves correctly if no mask was used before.
26 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Support for reading/writing MNI .obj surfaces
25 Mar 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add -nobout option, to suppress baseline betas from -Rbeta/-Obeta.
Per the request of Michael S Beauchamp, University of Texas.
25 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
+view now comes from data: so it works with +tlrc
24 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
by default now, no mask is applied in the scale and regression steps
Also added -regress_apply_mask option.
20 Mar 2009, RC Reynolds, @build_afni_Xlib, level 2 (MINOR), type 1 (NEW_PROG)
moved from X/@build.Xlib, for distribution
and added to SCRIPTS for building afni_src.tgz in Makefile.INCLUDE
19 Mar 2009, RC Reynolds, 1d_tool.py, level 3 (MAJOR), type 1 (NEW_PROG)
added lib_afni1D.py and 1d_tool.py
This is a library and tool for manipulating 1D files.
Many functions will still be added.
19 Mar 2009, RC Reynolds, eg_main_chrono.py, level 2 (MINOR), type 2 (NEW_OPT)
added -verbose_opts option, for being verbose during option processing
19 Mar 2009, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
a few additions and changes
- allow container chars (e.g. []) in decode_1D_ints()
- added is_valid_int_list()
- changed str vars to istr (as str is a keyword)
18 Mar 2009, RC Reynolds, eg_main_chrono.py, level 2 (MINOR), type 1 (NEW_PROG)
sample main python program using a library and chronological options
18 Mar 2009, DR Glen, 3dZcat, 3daxialize, level 2 (MINOR), type 2 (NEW_OPT)
NIFTI support
Fixed support for NIFTI output in 3dZcat and 3daxialize
Added -frugal option to 3daxialize to keep old behavior
for AFNI format datasets. Existing -frugal option in
3dZcat imposes 'oldish' behavior too.
16 Mar 2009, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
malloc extra val in case of percentile truncation
12 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
SUMA talks to matlab.
12 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
warn user about masking in orig space
- if despiking and no regression mask, apply -nomask
- added 'MASKING NOTE', to suggest no regresion mask until group space
12 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_reml_exec and -regress_3dD_stop
One can execute 3dREMLfit and/or 3dDeconvolve. Error blur is from each.
11 Mar 2009, RW Cox, 3dANOVA, level 2 (MINOR), type 2 (NEW_OPT)
Add -mask option to 3dANOVA, 3dANOVA2, 3dANOVA3
10 Mar 2009, DR Glen, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
Sum option
Sum option (for functional weighting of interiorosity measure)
06 Mar 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Add 'WAV' function (from waver) to -stim_times repertoire.
06 Mar 2009, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
if mri_automask_image() input is not really 3D, only apply clip
3dD uses automask for misfit warning, let this apply to niml.dset
05 Mar 2009, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
free vox_warp via KILL_list rather than directly when deleting dataset
Fixes afni crash: set acpc markers -> acpc view -> orig view
-> new markers -> acpc view -> death ...
04 Mar 2009, RC Reynolds, X-general, level 2 (MINOR), type 5 (MODIFY)
added openmotif build tree, updated @build.Xlib and README under X
03 Mar 2009, RC Reynolds, @build.Xlib, level 2 (MINOR), type 1 (NEW_PROG)
this is a build script for the local X packages
02 Mar 2009, RW Cox, zfun, level 2 (MINOR), type 0 (GENERAL)
add compression functions (using zlib) to libmri in zfun.c
27 Feb 2009, RC Reynolds, X-general, level 2 (MINOR), type 5 (MODIFY)
added lesstif and libXt trees to cvs
11 Feb 2009, RW Cox, 3dvolreg, level 2 (MINOR), type 4 (BUG_FIX)
replace DMAT_svdrot_old with DMAT_svdrot_newer
Old function fails sometimes, making the output rotation be garbage and
producing junk image results; the newer one seems more robust.
09 Feb 2009, RW Cox, imseq.c, level 2 (MINOR), type 3 (NEW_ENV)
Add AFNI_ANIM_DUP environment variable.
Allows user to duplicate images when writting an animation (AGIF or
MPEG) file. A simple and stoopid way to slow down an MPEG.
09 Feb 2009, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 5 (MODIFY)
random updates, plus those for Fedora 10
04 Feb 2009, RC Reynolds, vol2surf, level 2 (MINOR), type 4 (BUG_FIX)
fixed norm reversal application and norm dir check computation
Thanks to Xiaopeng Zong for finding these problems.
02 Feb 2009, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT)
SurfDist now outputs distances from one node to a set of other nodes
02 Feb 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added load_col option to DriveSuma
02 Feb 2009, RW Cox, parser (calc programs), level 2 (MINOR), type 5 (MODIFY)
Add hrfbk4 and hrfbk5(t,T) functions to parser
To imitate the BLOCK4 and BLOCK5 response functions in 3dDeconvolve.
13 Jan 2009, ZS Saad, afni-matlab, level 2 (MINOR), type 1 (NEW_PROG)
Added GS_orth_1D.m to perform Gram-Schmidt orthogonalization
13 Jan 2009, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
AFNI should now be Lesstif compliant
Made numerous changes with Rick Reynolds. The biggest modification
regards buttons inside popup menus. Those buttons are no longer
inside rowcolumn widgets and had to be directly managed by afni.
05 Jan 2009, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT)
Program no longer confined to FreeSurfer surfaces
The program now allows the user to specify any morph sphere,
not just sphere.reg or sphere. This required rewriting much of
of the program's main section but the algorithm for the mapping
remains unchanged.
31 Dec 2008, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
fix for lesstif crash on 'where am i', along with ziad
30 Dec 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 5 (MODIFY)
For FALTUNG, use sparse matrix operations for pure least squares.
Deconvolution + penalty matrix is sparse. Uses the 'rcmat' functions
originally developed for 3dREMLfit. Speeds things up a lot when the
time series is long.
22 Dec 2008, G Chen, 3dICC.R, level 3 (MAJOR), type 1 (NEW_PROG)
IntraClass Correlation (ICC)
This is an R program that calculates ICC on 3D volume data based on a
two- or three-way random-effects ANOVA scheme. See more details at
http://afni.nimh.nih.gov/sscc/gangc/ICC
16 Dec 2008, G Chen, 3dGC.R, level 3 (MAJOR), type 1 (NEW_PROG)
Bivariate Granger causality analysis
This is an R program that runs Granger causality analysis with a
seed region versus the rest of the brain. See more details at
http://afni.nimh.nih.gov/sscc/gangc/3dGC
13 Dec 2008, ZS Saad, afni-matlab, level 3 (MAJOR), type 1 (NEW_PROG)
RetroTS creates regressors for cardiac, respiratory, and RVT filtering
RetroTS.m and accompanying functions create slice-based regressors
for regressing out the effects of cardiac, respiratory, and RVT effects
from FMRI time series. The regressors generated are meant to be used
with 3dREMLfit.
11 Dec 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed -slibase bug.
Oopsie. -slibase didn't work properly with more than 1 added column per
slice. Also, per the request of ZSS, you can now input more than 1
column set per image file, in repetitive slice order:
0 1 2 3 0 1 2 3 0 1 2 3
if there are 4 slices in the dataset, for example.
10 Dec 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added new options for extra stimuli, RONI and an external volreg base
- allow NIfTI datasets as input (but process as AFNI)
- added -regress_extra_stim_files and -regress_extra_stim_labels
- added -regress_RONI and -volreg_base_dset (for Jill Weisberg)
09 Dec 2008, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed (potential) SUMA crash when Draw ROI interface is first opened
09 Dec 2008, ZS Saad, @Align_Centers, level 2 (MINOR), type 2 (NEW_OPT)
Added -cm option to allow centering based on the center of mass
09 Dec 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
Added 'dmBLOCK' to the '-stim_times_IM' repertoire.
05 Dec 2008, DR Glen, to3d, level 2 (MINOR), type 5 (MODIFY)
Siemens DICOM handling
added -oblique_origin and -reverse_list to help handle Siemens
DICOM data. oblique_origin option added to to3d and 3drefit
Rick added flipped slice handling to oblique mosaic handling
04 Dec 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Extend -stim_times_AM2 option to allow multiple amplitudes
04 Dec 2008, RW Cox, 1dMarry, level 2 (MINOR), type 5 (MODIFY)
Allow multiple marriages, to go with 3dDeconvolve changes
04 Dec 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
added balloon target for M Belmonte
Also modified Makefile.linux_xorg7_64 and macosx_10.4_G5/Intel and 5_Int*.
02 Dec 2008, ZS Saad, SpharmReco, level 3 (MAJOR), type 1 (NEW_PROG)
Reconstructs data from spherical harmonics decomposition.
See SpharmDeco -help and the demo script @Spharm.examples
for details.
02 Dec 2008, ZS Saad, SpharmDeco, level 3 (MAJOR), type 1 (NEW_PROG)
Performs spherical harmonics decomposition.
This program performs spherical harmonics decomposition
for surfaces' geometry and/or surface-based data
See SpharmReco -help and the demo script @Spharm.examples
for details.
02 Dec 2008, ZS Saad, @Spharm.examples, level 3 (MAJOR), type 1 (NEW_PROG)
A script to demonstrate the usage of SpharmDeco and SpharmReco
02 Dec 2008, ZS Saad, @NoisySkullStrip, level 3 (MAJOR), type 1 (NEW_PROG)
A script to improve skull stripping in noisy of heavily shaded data
01 Dec 2008, RC Reynolds, timing_tool.py, level 3 (MAJOR), type 1 (NEW_PROG)
a tool for manipulating and evaluating stimulus timing files
This is useful for getting statistics on rest timing.
24 Nov 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added options -infile_list and -show_sorted_list
The -show_sorted_list option will print a list of files by run/index.
21 Nov 2008, ZS Saad, @fast_roi, level 3 (MAJOR), type 1 (NEW_PROG)
Creates Atlas-based ROIs in original space for real-time experiments
21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added Options menu, Show Cosmat and GUI help
This is the initial release version, 1.0.
21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -test_libs option
21 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT)
removed 'R' from basic test list, and applied verb 2 to base usage
20 Nov 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
incorportated real-time volume writing from V. Roopchansingh of MCW
18 Nov 2008, RW Cox, 3dANOVA programs, level 2 (MINOR), type 2 (NEW_OPT)
Add option to output float-valued datasets.
Set the AFNI_FLOATIZE environment variable to YES, and the output of
3dANOVA, 3dANOVA2, and 3dANOVA3 will be stored in float format instead
of in scaled short format. [Per the request of Paul Hamilton]
18 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -test, -show_col_types, -show_cosmat, -show_fit_ts, -cormat_cutoff
also added the main help
13 Nov 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added a NIDO sphere as Displayable Object
See suma -help_nido for details.
13 Nov 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -al option to use 3dAllineate -lpa
07 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 5 (MODIFY)
more updates:
- scipy is only tested for when necessary
- compute norms locally if no scipy
- solve_against_1D, linear_combo: return error string instead of code
- added -chrono option, to make all options chronological
(so options are essentially scriptable)
07 Nov 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
tlrc view handling
fixed view name of tlrc output with tlrc_master set to SOURCE
06 Nov 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 0 (GENERAL)
Add 'scale to shorts misfit' warning messages.
Also added to 3dcalc and some other programs.
06 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
pre-release updates:
- added many initial command-line options
- added plot_xmat_as_one toggle button
- added computation of cosine matrix and cosmat_warnings
- separated GUI code into new file gui_xmat.py
06 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -full_test
06 Nov 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Oblique children handling
fixed combination of oblique with child epis for epi2anat output
04 Nov 2008, RW Cox, 3dNLfim, level 2 (MINOR), type 0 (GENERAL)
Added model_expr2.c
Model that uses an arbitrary 3dcalc-like expression with 2 free
parameters (any letters but 't', which is used for the time axis).
04 Nov 2008, RW Cox, 3dBlurToFWHM, level 2 (MINOR), type 4 (BUG_FIX)
skip all zero sub-bricks in the blurmaster - for Tomski Rosski
03 Nov 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Several changes
Finished -gltsym, -Rglt, and -Oglt options = add GLTs on the 3dREMLfit
command line and output those exclusively to new files.
Modified -addbase and -slibase to do censoring if input 1D files are the
same length as the uncensored matrix.
Also fixed bugs in -ABfile. Oopsie.
31 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_timing_stats option
Also, made a small change affecting timing (old results will not match).
31 Oct 2008, DR Glen, 3drefit, level 2 (MINOR), type 5 (MODIFY)
Time axis attributes
Added support in 3drefit for applying time axis attributes
30 Oct 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
AddEdge with epi2anat
fixed AddEdge option for epi2anat output
29 Oct 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 5 (MODIFY)
if the X-matrix has a constant regressor, do not de-mean it
In such a case, the cormat would not exactly be a correlation matrix.
29 Oct 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 1 (NEW_PROG)
program to test python module imports (interface to module_test_lib.py)
28 Oct 2008, RC Reynolds, module_test_lib.py, level 2 (MINOR), type 1 (NEW_PROG)
library to test python module imports
One might want to apply this module at the top of any python file.
27 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -offset option
27 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX)
actually applied -min_rest, sorry...
27 Oct 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_motion_file option
24 Oct 2008, RC Reynolds, xmat_tool.py, level 4 (SUPER), type 1 (NEW_PROG)
program to inspect a .xmat.1D X-matrix, possibly against a time series
This is a Graphical tool for plotting a design matrix, reviewing
condition numbers or the correlation matrix, and fitting to a 1D
time series.
23 Oct 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Added -rout option, by popular 'demand'
23 Oct 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 4 (BUG_FIX)
removed reference to cdflib, for 'make afni_src.tgz'
20 Oct 2008, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
added write_text_to_file function
20 Oct 2008, RC Reynolds, afni_driver.c, level 2 (MINOR), type 2 (NEW_OPT)
added 'GETENV' to the list of DRIVE_AFNI commands
15 Oct 2008, RW Cox, fdrval, level 2 (MINOR), type 1 (NEW_PROG)
Compute FDR value on command line, from dataset header
15 Oct 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed errts (etc) outputs: censored values not set to zero!
15 Oct 2008, DR Glen, afni plugouts, @AddEdge, level 2 (MINOR), type 5 (MODIFY)
quiet communications
@AddEdge silences communications as plugout
14 Oct 2008, RW Cox, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
If source=scaled shorts, then output will be scaled as well.
14 Oct 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor updates
AddEdge option enhanced and help updated
14 Oct 2008, DR Glen, @AddEdge, level 2 (MINOR), type 5 (MODIFY)
Help and options
More user options, improved help, removed temporary files
09 Oct 2008, G Chen, 1dGC.R, level 4 (SUPER), type 1 (NEW_PROG)
Multivariate Granger causality analysis
This is an R program that runs Granger causality analysis among a few
pre-select regions. See more details at
http://afni.nimh.nih.gov/sscc/gangc/1dGC
06 Oct 2008, DR Glen, 3drefit, level 2 (MINOR), type 5 (MODIFY)
-atrfloat and -atrint options
Allows addition and modification of dataset attributes
including modifying IJK_TO_DICOM_REAL. Not all attributes
can be modified if fairly basic to dataset.
03 Oct 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
SUMA accepts text, images, and textures as Displayable Objects
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects (DOs). The new DOs are in a simple
NIML format. It is simplest to look at the script @DO.examples
for illustrations of the various forms of DOs that SUMA supports.
Sample NIML DOs (called NIDOs) are now provided with the distribution
They are called demo.*.niml.do.
03 Oct 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
-viewer_position/_width/_height/_size to control window placement
See DriveSuma -help for details.
03 Oct 2008, ZS Saad, @DO.examples, level 2 (MINOR), type 1 (NEW_PROG)
A script that demonstrates the use of Displayable Objects
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects (DOs).
30 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -gltsym option
Makes it easy for the user to add GLTs without using 3dDeconvolve.
29 Sep 2008, RC Reynolds, 3dmatmult, level 3 (MAJOR), type 1 (NEW_PROG)
program to multiply AFNI datasets slice-by-slice as matrices
26 Sep 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
-child_anat option
Convenience option to align follower anat datasets to epi
25 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -usetemp option
Saves REML setup matrices for various cases to tmp disk files. Is
necessary for -slibase and -Grid 5 combined, if anyone ever actually
wants to run such a case.
24 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
-addbase and -slibase options to add baseline columns to matrix
In particular, -slibase is intended for per-slice modeling of
physiological noise effects. Sucks up a lot of memory and CPU time.
23 Sep 2008, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
save last jumpto_xyz string, etc.
23 Sep 2008, RC Reynolds, gen_epi_review.py, level 2 (MINOR), type 5 (MODIFY)
in script, check for existence of given datasets
23 Sep 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -remove_preproc_files option (akin to -move_preproc_files)
19 Sep 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
-giant_move option
For data that are very far apart
Fixed bug using long path names
18 Sep 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
More options
Intermediate file saved optionally now,
partial_axial,sagittal,coronal options
Edge-based method, nocmass default, resample step optional,
Added options to support searching for smaller structures,
3dWarpDrive can be used optionally as volume registration program
prep_off option to turn off several preprocessing steps
AddEdge option uses simplified names in output in new directory
17 Sep 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 2 (NEW_OPT)
added -labels option, for including labels in filenames
16 Sep 2008, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT)
-node_path_do outputs the shortest path between two nodes
The shortest path(s) are stored as a SUMA Displayable Object
which can be loaded into SUMA with ctrl+alt+s or using DriveSuma.
16 Sep 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
-load_do sends SUMA Displayable Objects to be rendered
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects.
16 Sep 2008, RC Reynolds, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
allow attribute editing of NIfTI datasets
15 Sep 2008, RW Cox, Draw Dataset plugin, level 2 (MINOR), type 5 (MODIFY)
Keystrokes F3 and F3 now decrement/increment drawing value in plugin
02 Sep 2008, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 4 (BUG_FIX)
Starting sphere center was incorrectly initialized
29 Aug 2008, ZS Saad, ExamineXmatR, level 3 (MAJOR), type 1 (NEW_PROG)
An interactive tool to examine a design matrix
29 Aug 2008, ZS Saad, 3ddelay, level 2 (MINOR), type 4 (BUG_FIX)
Unitialized pointer in 3ddelay
29 Aug 2008, RC Reynolds, vol2surf, level 2 (MINOR), type 5 (MODIFY)
fill in COLMS_STATSYM attribute when writing .niml.dset dataset
29 Aug 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
Feature size, AddEdge, skullstrip,rat options
Added options to support searching for smaller structures,
an option for rat brain alignment, alternate options for 3dSkullstrip
and an optional call for @AddEdge
28 Aug 2008, RW Cox, 3dAllineate, level 3 (MAJOR), type 5 (MODIFY)
A number of changes to improve robustness.
* Don't smooth noise added to source image outside of the mask
* Reduce default smoothing level for -lpc in coarse pass
* Increase number of points used for matching in the coarse pass
* More refinements of the twobest results in the coarse pass
* Refinements (-num_rtb option) of the twobest results in the fine pass
All this adds CPU time, but seems to make the program more reliably
convergent. Also:
* Restored operation of the -check option, to restart the optimization
at the final solution with other methods, to see what results they
give compared to the original method.
27 Aug 2008, DR Glen, 3danisosmooth, level 2 (MINOR), type 4 (BUG_FIX)
Initialized variable for 3D case
26 Aug 2008, RW Cox, 3dTcorrMap, level 2 (MINOR), type 1 (NEW_PROG)
Average correlations with every other voxel time series.
Kind of slow. For Kyle Simmons. And I still don't recognize Missouri!
26 Aug 2008, RC Reynolds, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
initialized ntask in all cases
25 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Added residual outputs to 3dREMLfit.
22 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add FDR curves and -?fitts options.
22 Aug 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added DRIVE_WAIT command string
The command will be executed after the first volume is processed,
which is good for opening windows appropriate to a new dataset.
21 Aug 2008, RW Cox, 3dREMLfit, level 4 (SUPER), type 1 (NEW_PROG)
Program to mimic 3dDeconvolve, but with serial correlations
Uses ARMA(1,1) model of noise, separately for each voxel.
21 Aug 2008, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
in edt_dsetitems, if storage mode can be inferred from prefix, apply it
21 Aug 2008, RC Reynolds, afni, level 2 (MINOR), type 2 (NEW_OPT)
added -disable_done option to safeguard real-time mode
21 Aug 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
use DSET_BRIKNAME for dataset control, as that is updated for smode
18 Aug 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
increase DRIVE_LIMIT to 4Kb, read env vars each run
These variables can now be controlled through drive_afni 'SETENV'
(either via 'plugout_drive' or 'Dimon -drive_afni'):
- AFNI_REALTIME_Mask_Vals : specify what gets sent to serial_helper
- AFNI_REALTIME_SHOW_TIMES : specify whether to show data timestampts
- AFNI_REALTIME_SEND_VER : specify whether to send comm version
15 Aug 2008, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
init graph->grid_spacing, to prevent potential div by 0 via DRIVE
14 Aug 2008, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
do not automatically print -max along with -var
05 Aug 2008, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
re-added the un16 fix from July 1
03 Aug 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 5 (MODIFY)
added swap ability for ANALYZE 7.5 format, and made swapping complete
- added nifti_analyze75 struct
- modified swap_nifti_header to swap all fields (analyze or nifti)
- added regression testing script c16.rand.swap
These changes were motivated by C Burns.
03 Aug 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -help_ana, -disp_ana, -swap_as_analyze, -swap_as_nifti, -swap_as_old
31 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 2 to work as -disp_all
See 'HELLO versions' from 'serial_helper -help' for details.
See 'example E' from 'Dimon -help' for a complete testing example.
31 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
enhancements to communication with serial helper
- added 'Motion Only' to methods
- parameter methods can easily be switched per run
- SEND_VER replaces HELLO_VER as Y/N variable
31 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -num_slices option, and full real-time example E
30 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 1 and -show_times option
30 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 1 and show_times option
These are set via AFNI_REALTIME_SEND_VER and AFNI_REALTIME_SHOW_TIMES.
29 Jul 2008, ZS Saad, afni, level 2 (MINOR), type 5 (MODIFY)
Changed transform used to crete mni coord. in interactive whereami
The transform from TLRC to MNI used to be via the manually TLRCed
N27 brain. However this created inconsistency in the second line of the
Focus point output (MNI Brain) on the order of a couple of mm
with the command-line whereami program.
Now both interactive and command-line whereami produce the same
Focus Point output. Note that the rest of the whereami
output remains unchanged.
29 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 5 (MODIFY)
captured and output more signal and error info, flushed output buffer
29 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
print more socket error info, send MP vals w/out mask
28 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 4 (BUG_FIX)
alter check for bad socket: use tcp_alivecheck over tcp_writecheck
28 Jul 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
Pre and post transformation matrices
Allow pre-transformation matrix instead of oblique transformation
and post-transformation instead of tlrc transformation.
Fixed concatenated matrices for oblique data. Master options
allow specification of dimension size on output. Script arguments
saved in output dataset.
25 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
allow -sleep_vol to be very small without early run termination
23 Jul 2008, RC Reynolds, 3dttest, level 2 (MINOR), type 2 (NEW_OPT)
added -base1_dset option, where -base1 value can vary over voxels
Added for M Beauchamp.
18 Jul 2008, RC Reynolds, 3dNLfim, level 2 (MINOR), type 5 (MODIFY)
listed signal and noise models in -help output
18 Jul 2008, DR Glen, to3d, level 2 (MINOR), type 5 (MODIFY)
Reverse order of slices in Siemens Mosaic data
Some Siemens Mosaic data can be in reverse order depending upon
obscure Siemens private DICOM tags.
Thanks to Doug Greve in Freesurfer group for edifying this situation
17 Jul 2008, RC Reynolds, 3dNLfim, level 2 (MINOR), type 5 (MODIFY)
warn the user if DSET_NVALS is not the same as DSET_NUMTIMES
That would suggest the dataset has no time axis.
16 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added -disp_all to give formatted display of 'all' mask data
This was added for P Kundu.
16 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added choice of 'Vals to Send' to serial_helper
Can now send index,i,j,k,x,y,z,value for every value in mask.
15 Jul 2008, DR Glen, general, level 2 (MINOR), type 5 (MODIFY)
Can turn off all obliquity warnings
AFNI_NO_OBLIQUE_WARNING variable is extended to turn off warnings
about using oblique data in commandline programs and in GUI
15 Jul 2008, DR Glen, 3dWarp, level 2 (MINOR), type 4 (BUG_FIX)
Print correct obliquity transformation matrix
14 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
terminate TCP transmission to serial_helper if mask is bad
14 Jul 2008, RC Reynolds, afni_history, level 2 (MINOR), type 5 (MODIFY)
a single integer option is interpreted as with -past_entires
14 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -sleep_init, -sleep_vol, -sleep_frac
These options control the timeout periods between data checks.
10 Jul 2008, RC Reynolds, plug_realtime, level 3 (MAJOR), type 5 (MODIFY)
receive oblique transform matrix via new OBLIQUE_XFORM interface
10 Jul 2008, RC Reynolds, Dimon, level 3 (MAJOR), type 5 (MODIFY)
if the data is oblique, pass the transformation matrix to plug_realtime
01 Jul 2008, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
fixed crash in case of mosaic and un16, no longer having im data
Problem found by R. McColl.
01 Jul 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
modified the make system for building programs in the install directory
- modified Makefile.INCLUDE's INFLAGS and ISFLAGS
- modified SUMA_INPATH in SUMA_Makefile_NoDev.
- removed 'rickr/' dirs from includes in mrilib.h, plug_crender.c and
3dAllineate.c
Requested by V. Roopchansingh of MCW.
30 Jun 2008, RC Reynolds, gen_epi_review.py, level 2 (MINOR), type 5 (MODIFY)
make script executable, decrease sleep, add usage comment in script
30 Jun 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -gen_epi_review and -no_epi_review options
By default, a drive_afni script to review EPI data is now generated.
27 Jun 2008, RC Reynolds, gen_epi_review.py, level 3 (MAJOR), type 1 (NEW_PROG)
generate afni/drive_afni script to review initial EPI data
This program was written to be called from the afni_proc.py output script.
25 Jun 2008, RC Reynolds, howto, level 2 (MINOR), type 5 (MODIFY)
put disclaimers at the tops of HowTo #1, #2, and #5
references to current AFNI class handouts were included
25 Jun 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -past_entries option
24 Jun 2008, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Extend max number of clusters reportable, for Shruti.
24 Jun 2008, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
added the ability to output 1D iresp datasets
20 Jun 2008, RC Reynolds, libmri, level 2 (MINOR), type 5 (MODIFY)
thd_niftiread: do not scale to float if scale=1 and inter=0
19 Jun 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 5 (MODIFY)
help update, added -show_valid_opts, use '*' as separator w/amplitudes
18 Jun 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixes - duplicate master options, mislabeled variable
16 Jun 2008, RC Reynolds, file_tool, level 2 (MINOR), type 5 (MODIFY)
show output for multiple bad files when using -show_bad_backslash
13 Jun 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 2 (NEW_OPT)
added nifti_compiled_with_zlib()
13 Jun 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -with_zlib, and ability to add extensions via 'file:FILENAME'
extension update added for J. Gunter
13 Jun 2008, RC Reynolds, 3dclust, level 2 (MINOR), type 5 (MODIFY)
in the help, Volume defaults to microliters, unless -dxyz=1 is used
12 Jun 2008, RC Reynolds, neuro_deconvolve.py, level 2 (MINOR), type 1 (NEW_PROG)
generate 3dTfitter script to deconvolve a BOLD signal into a neuro signal
11 Jun 2008, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 5 (MODIFY)
Obliquity handling in alignment, more grid options
10 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 2 (NEW_OPT)
Add -ARMA option to estimate ARMA(1,1) parameters
06 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation matrix of a time series, averaged locally.
06 Jun 2008, RW Cox, 3dErrtsCormat, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation matrix of a time series, globally.
06 Jun 2008, RC Reynolds, plug_crender, level 2 (MINOR), type 4 (BUG_FIX)
integral threshold was off by 1
29 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 5 (MODIFY)
allowed for -polort -1 and for sub-brick selection with dataset names
22 May 2008, RC Reynolds, 3dTshift, level 2 (MINOR), type 4 (BUG_FIX)
with -rlt, slices without any time shift must still be processed
problem noticed by Jie Huang
21 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed incorrect scaling in Cp computation
The error was introduced on April 8, 2008.
20 May 2008, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
Clusterize: '-' as the filename means write to stdout.
18 May 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added options for TR-locking and storing '3dDeconvolve -nodata' examples
- added shuffle() to replace that from random (cannot produce all perms)
- added options -tr, -tr_locked and -save_3dd_cmd
- changed -stim_time option to -stim_dur
17 May 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
check result of 3dDeconvolve execution in output script
If 3dDeconvolve fails, terminate the script so that the user can
see what happened.
15 May 2008, ZS Saad, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
added -n_rand and -n_randseed
15 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 4 (BUG_FIX)
Fixed memory corruption when using more than 20 regressors
14 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed application of decay term
14 May 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
1D file names for child epi data,micro changes
13 May 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -set_extern_filelist option, and help for using external data files
13 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
gifticlib-1.0.0: initial release
includes support for (set/clear/read/write) external data files
09 May 2008, ZS Saad, 3dROIstats, level 3 (MAJOR), type 2 (NEW_OPT)
Added option -1Dformat to output results in 1D format
09 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
gifticlib-0.0.18: giiCoordSystem is now an array of struct pointers
modified GIFTI library, along with suma_gifti.c
08 May 2008, ZS Saad, 3dsvm, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed memory corruption caused by improper declaration of combName
08 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 5 (MODIFY)
updated help, NFIRST does not need to imply injection time
07 May 2008, RC Reynolds, make_random_timing.py, level 3 (MAJOR), type 1 (NEW_PROG)
generate random stimulus timing files
This generates random timing files suitable for use in 3dDeconvolve.
The timing is not restricted to a TR grid, though that is possible.
Consider use with '3dDeconvolve -nodata'.
07 May 2008, RC Reynolds, plug_3Ddump_V2, level 2 (MINOR), type 4 (BUG_FIX)
allow 4D datasets to be opened (so that buckets are again usable)
PLUGIN_dset_check() now checks NVALS instead of NUM_TIMES...
07 May 2008, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT)
added get_type_list and other accessor functions
01 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
treat RESID_CT as Ct(t), not C(t)
30 Apr 2008, RW Cox, mcw_glob.c, level 2 (MINOR), type 3 (NEW_ENV)
setenv AFNI_SHELL_GLOB YES == wildcard expansion via the shell
For Graham Wideman and Mac OS X Server 10.5 problems.
17 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor changes
Child epi datasets can be volume registered even if parent epi
is a single sub-brick
16 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
multiple changes
Naming conventions for tlrc output, generic shell compatible,
regridding options for epi and tlrc epi output
14 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
minor change
3dAllineate options are also applied to epi to anat alignment,
so output EPI datasets get original resolution and type.
10 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor changes
remove tabs in file, change output file names for epi children,
changes to help, and renamed tlrc parent option
08 Apr 2008, RW Cox, 3dUpsample, level 2 (MINOR), type 1 (NEW_PROG)
Upsample a 3D+time dataset (in the time direction)
08 Apr 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 3 (NEW_ENV)
allow residual Ct values via AFNI_MODEL_D3_RESID_CT_DSET dataset
e.g. setenv AFNI_MODEL_D3_RESID_CT_DSET residual_Ct+orig
08 Apr 2008, RC Reynolds, 2dImReg, level 2 (MINOR), type 4 (BUG_FIX)
allow zero slices, passing input as result
Choleski factorization would fail on an empty slice. In this case,
return the input slices as the result (instead of crashing).
Done with D Glen.
07 Apr 2008, RW Cox, 1dUpsample, level 2 (MINOR), type 1 (NEW_PROG)
Upsample a 1D time series
07 Apr 2008, DR Glen, align_epi_anat.py, level 4 (SUPER), type 1 (NEW_PROG)
Alignment of EPI and Anatomical datasets
Aligns anat and EPI data. Alignment is in either direction of anat to
epi or epi to anat. Transformations are combined where possible as
from time series registration and talairach transformations. Multiple
child epi datasets may be aligned at the same time.
04 Apr 2008, RW Cox, 3dAllineate, level 2 (MINOR), type 0 (GENERAL)
Added '-nwarp bilinear' option
Experimental nonlinear warping comes to 3dAllineate at last.
Preliminary test looks good, but more work is needed to be sure it's OK.
02 Apr 2008, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Changed suma -environment's output to reflect user's current environment.
With this change, users can always replace their .sumarc with
the one output by suma -environment without worrying about loosing
their preferred settings.
02 Apr 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
extended maximum number of contrasts to 75
01 Apr 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
increased internal memory for 3dbucket and 3drefit command creation
31 Mar 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
extended maximum number of means, diffs and contrasts to 50
28 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -copy_gifti_meta and -copy_DA_meta options
28 Mar 2008, DR Glen, 3dDTeig, level 2 (MINOR), type 4 (BUG_FIX)
small negative eigenvalues are set to zero as in 3dDWItoDT
This fix avoids FA being set to 0 for those affected voxels
27 Mar 2008, ZS Saad, afni-matlab, level 2 (MINOR), type 5 (MODIFY)
Added other return options for Read_1D.m and BrikLoad.m
26 Mar 2008, ZS Saad, cat_matvec, level 2 (MINOR), type 5 (MODIFY)
cat_matvec can now output IJK_TO_CARD_DICOM and IJK_TO_DICOM_REAL
26 Mar 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -align_centers as an option to deal with very large moves
It used to be that users had to run @Align_Centers on all their
data when big moves were needed to align the surface's antaomy
to that of the experiment. This is no longer needed.
26 Mar 2008, ZS Saad, @Align_Centers, level 2 (MINOR), type 5 (MODIFY)
Script now outputs a matrix that represents the shift
This matrix can be used with 3dAllineate to perform the shift.
26 Mar 2008, ZS Saad, 3dvolreg, level 2 (MINOR), type 4 (BUG_FIX)
3dvolreg's -1Dmatrix_save was not always accounting for centers of rotation
Now the output of -1Dmatrix_save always matches what one would get for
the first sub-brick from
cat_matvec FRED+orig::VOLREG_MATVEC_000000 -I
26 Mar 2008, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
Add -norm2 and -normx options: normalize time series before plotting
26 Mar 2008, DR Glen, python, level 2 (MINOR), type 4 (BUG_FIX)
repaired support for dry_run mode in python scripts
25 Mar 2008, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Instead of SAME, one can use surface's name as LocalDomainParent
25 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
ROIs drawn on different surfaces now handled properly
25 Mar 2008, RW Cox, 3dDetrend, level 2 (MINOR), type 4 (BUG_FIX)
-normalize didn't work -- what the hellll was I thinking?
Also, added some help to explain how to use 3dDetrend on 1D files.
25 Mar 2008, RW Cox, 1dnorm, level 2 (MINOR), type 4 (BUG_FIX)
Forgot the sqrt()! kudos to David Perlman.
25 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 5 (MODIFY)
the -compare_data option is not separate from -compare_gifti
25 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
minor changes:
- NIFTI_INTENT_NONE is considered valid
- added compare_gifti_data functions
- LabelTables are now written using CDATA
24 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 5 (MODIFY)
deconvolution with penalty factor = 0 is modified
Now the criterion for choosing the penalty factor is based on curvature
rather than distance from the origin. Seems to be more robust, but
probably will require yet more tweaking.
24 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added GERT_Reco options (request of D Glen)
-gert_filename : specify a name for the GERT_Reco script
-gert_nz : override nz=1 in mosaic image files
-gert_to3d_prefix : specify a dataset prefix for the to3d command
24 Mar 2008, RC Reynolds, @Align_Centers, level 2 (MINOR), type 4 (BUG_FIX)
applied proper follower dataset orientation and floating point shifts
The shift applied to the child datasets was based on the parent's
orientation. The shifts were also being truncated to integers.
Changed with D Glen.
20 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
Add -polort option, to keep Gang Chen happy.
20 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_WRITE_1D_AS_PREFIX allows writing 1D or surface data given the prefix
For example, setting this to YES will allow writing surface data to NIfTI.
18 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -compare_gifti option
See 'gifti_tool -help' for details, including example #7.
18 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added comparison functions to gifticlib
17 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if 1 volume, GERT_Reco_dicom does not give (useless) timing to to3d
13 Mar 2008, RC Reynolds, 3dmerge, level 2 (MINOR), type 0 (GENERAL)
added some examples to the -help output
12 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Changed surface controller font to 8.
You can get the old font size with environment
variable SUMA_SurfContFontSize BIG.
The default is now SMALL.
11 Mar 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 2 (NEW_OPT)
added control of hematocrit via AFNI_MODEL_D3_HCT
10 Mar 2008, RC Reynolds, SUMA_SurfMeasures, level 3 (MAJOR), type 4 (BUG_FIX)
averages did not include nodes lost to -cmask
Noticed by M Beauchamp.
10 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_GIFTI_VERB sets the verbose level in the gifti I/O library
The default is 1, 0 is quiet, and values go up to 7.
10 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 0 (GENERAL)
AFNI can read/write .gii.dset as with .gii
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
applied -gert_outdir in the case of dicom images
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if only 1 run, GERT_Reco_dicom is named per run
07 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Color map in surface controller can be flipped and rotated
* f key for flipping colormap
* Up/Down keys for rotating color map
* Home for home
Hit ctrl+h on Surface Controller's colormap for more help.
07 Mar 2008, RW Cox, Dataset#N, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_DATASETN_NMAX sets number of datasets allowed
New environment variable AFNI_DATASETN_NMAX sets the number of datasets
allowed in Dataset#N plugin, from 9..49. This is for Shruti.
07 Mar 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 4 (BUG_FIX)
properly ignore empty lines, and exit on short files
06 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Added three variables affecting the surface controller
* SUMA_ShowOneOnly: Sets '1 Only' on or off. On by default
* SUMA_GraphHidden: Update open graphs even if corresponding dset
is hidden.* SUMA_ColorMapRotationFraction: Fraction of
colormap to rotate
up or down with arrow keys.
See suma -environment for a complete list.
05 Mar 2008, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
Support for GIFTI surface format writing
GIFTI writing can now be done with SUMA programs.
For example, see options -o_gii and -xml* in ConvertSurface program.
05 Mar 2008, RW Cox, afni-general, level 2 (MINOR), type 5 (MODIFY)
Change the way 1D datasets are written to disk from 3D programs
In programs that analyze time series files (such as 3dTfitter), you can
input 1D files and make the column direction be the time axis by using
suffixing the file with \' -- but when it comes to writing the results
dataset out, the standard AFNI I/O method is to write the time axis
along the row direction. With this change, if you input a 1D file in
the place of a 3D dataset AND put '.1D' at the end of the output file
prefix, then the output dataset will be written so that the time axis
is along the column direction.
05 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
added '-fitts' option to produce fitted time series dataset
05 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixed passing of INDEX_LIST
05 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
do not duplicate data when reading and writing GIFTI from AFNI
04 Mar 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
couple of small changes to help the hapless users
* add more informative error message if allocate_memory() fails
* force '-float' if any output prefix is NIfTI-1 format (.nii)
04 Mar 2008, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
added -accumulate option, to output each partial sum
for k = 0..N-1 : output[k] = sum(input[i]) over i = 0..k
03 Mar 2008, RC Reynolds, website, level 2 (MINOR), type 5 (MODIFY)
updated the AFNI History website pages, with a table of entries
29 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added a TYPE, -type, a new level, and a string to identify each level
29 Feb 2008, G Chen, 3dICA.R, level 4 (SUPER), type 1 (NEW_PROG)
Independent component analysis
This is an R program that runs independent component analysis. It
takes one dataset that presumably has already been properly
pre-processed.already been properly pre-processed. See more details at
http://afni.nimh.nih.gov/sscc/gangc/ica.html
28 Feb 2008, ZS Saad, suma-general, level 3 (MAJOR), type 3 (NEW_ENV)
Support for GIFTI surface format reading
28 Feb 2008, RW Cox, 3dUndump, level 2 (MINOR), type 0 (GENERAL)
allow input of NO text files, to produce an 'empty' dataset
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow constraints on sign of deconvolved function
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow combination of penalty functions in deconvolution
28 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -list_authors option and adjusted spacing
27 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Addition of p and q values under threshold bar
Use BHelp on p and q text in suma to get more info.
27 Feb 2008, RW Cox, 3dTfitter, level 3 (MAJOR), type 2 (NEW_OPT)
add deconvolution via the '-FALTUNG' option
Unlike 3dDeconvolve, this deconvolution is to find the input time
series, given the impulse response function.
27 Feb 2008, RC Reynolds, afni_history, level 4 (SUPER), type 1 (NEW_PROG)
program to display the history of AFNI updates
This will be used to create a web page of AFNI updates.
Please see 'afni_history -help' for more details.
27 Feb 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed -regress_use_stim_files typo (was -regress_use_stim_times)
25 Feb 2008, RW Cox, 1dsvd, level 2 (MINOR), type 2 (NEW_OPT)
add '-vmean' and '-vnorm' options, to mirror capabilities in 3dpc
25 Feb 2008, RC Reynolds, plug_vol2surf, level 3 (MAJOR), type 4 (BUG_FIX)
fixed application of cluster for sending data to suma
Previously, clustering was only applied when the Olay and Thr sub-bricks
were the same.
24 Feb 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
GIFTI library now considers MetaData without Value as valid
22 Feb 2008, RW Cox, 3dpc, level 2 (MINOR), type 2 (NEW_OPT)
add '-eigonly' and '-reduce' options; output eigenvalues to a 1D file
'-eigonly' causes 3dpc to print eigenvalues to stdout and stop there.
'-reduce n pp' outputs a reduced dataset, using only the largest 'n'
eigenvalues.
21 Feb 2008, RC Reynolds, GIFTI, level 4 (SUPER), type 0 (GENERAL)
AFNI programs can now read and write GIFTI datasets
GIFTI datasets are for data in the surface domain, with file suffix .gii.
Support must be requested at compile time, and it requires libexpat.
Please see http://www.nitrc.org/projects/gifti for many details.
20 Feb 2008, RW Cox, 1deval, level 2 (MINOR), type 2 (NEW_OPT)
add '-1D:' option, to write output that is usable on the command line
Sample usage:
1dplot `1deval -1D: -num 71 -expr 'cos(t/2)*exp(-t/19)'`
The backquotes `...` capture command's output and put this string on
the command line. The '-1D:' option formats the 1deval output so that
it is ready to be used in this way.
16 Feb 2008, RW Cox, 3dTfitter, level 4 (SUPER), type 1 (NEW_PROG)
new program = linear fits to voxel time series
Uses L1 or L2 regression, with optional constraints to fit each voxel
time series as a sum of basis time series, which can be 1D files or
3D+time datasets. Basis time series that are 1D time series are
the same for all input voxels. Basis time series that are 3D+time
datasets are different for each voxel.
Differences from 3dDeconvolve:
* Basis time series can vary across voxels.
* Fit coefficients can be found with L1 or L2 error functions, and
can be constrained to be positive or negative.
* 3dTfitter does not compute goodness-of-fit statistics.
14 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Graphing of dset content with 'g'
A graph of the column content at a node can be plotted
This would be the surface equivalent to AFNI's graphing function.
See suma's interactive help 'ctrl+h' for more info.
12 Feb 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
An option to show all of suma's environment variables
See help for -environment in suma -help.
06 Feb 2008, ZS Saad, SurfDist, level 3 (MAJOR), type 1 (NEW_PROG)
Program to calculate geodesic internodal distances
06 Feb 2008, RC Reynolds, 3dbucket, level 2 (MINOR), type 0 (GENERAL)
modified to copy FDR curves
04 Feb 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_NEWSESSION_SWITCH in afni_func.c == switch to new session?
31 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify plug_crender.c to obey AFNI_SLAVE_THRTIME.
24 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add FDR curve generation to 3dANOVA.lib, 3dNLfim, 3dRegana, 3dttest.
* Fix little problems with AFNI threshold scale display as q-value alters.
* Fix bug in thd_mastery.c in assiging FDR curves to mastered sub-bricks.
* Add '-killSTAT' option to 3drefit.
23 Jan 2008, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* FDR thresh-vs-z(q) curve generation and storage in datasets.
* Display FDR q in AFNI pval label.
* Generate FDR curves automatically in 3dDeconvolve, and with
'-addFDR' option in 3drefit.
22 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Minor changes to 3dFDR: better help, -float, -qval.
* Add -sort and -SORT options to 3dcalc, for no good reason.
* Add 'help' command to ccalc, to give parser info.
22 Jan 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options to estimate smoothness in data for use in AlphaSim
See help options -regress_est_blur_epits and -regress_est_blur_errts.
17 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* AFNI_FLOATIZE environment variable for 3dDeconvolve.c and 3dcalc.c.
* mri_fdrize.c function for FDR-z conversion.
12 Jan 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Scroll lists for I T and B selectors in suma
Right click on pulldown menu titles to get
a scroll list instead. This makes selecting from
a long list of options, or columns, much easier.
Right click on 'I' to the left of suma's Intensity Selection
button for an illustration.
09 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* SIGQUIT delay in afni.c, for Jerzy.
28 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Popup menu in clusterize report to set histogram range.
28 Dec 2007, RC Reynolds, gifti_tool, level 3 (MAJOR), type 1 (NEW_PROG)
program to read and write GIFTI datasets
27 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Upgrades to clusterize reporting window: histograms, from/to indexes
on auxiliary dataset, 3dclust and save table buttons, &c.
* Fixed bug in DG's obliquity reporting function in thd_coords.c -- it
didn't check if the input dataset was valid -- caused AFNI to crash.
20 Dec 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* Clusterize reporting window.
19 Dec 2007, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
Use of '[i]' to select node index from surface dset
Square bracket '[]' selection works for surface-based
datasets much like it does for volume-based ones.
In addition, one can use '[i]' to select the indices
of nodes for which data are defined in a particular
surface-based dataset.
For more information, see 'SUMA dataset input options:'
section in the output of ConvertDset -help .
18 Dec 2007, ZS Saad, ROIgrow, level 2 (MINOR), type 1 (NEW_PROG)
Grows regions separately, depending on labels
18 Dec 2007, ZS Saad, ROI2dataset, level 2 (MINOR), type 0 (GENERAL)
Output full datasets if needed
17 Dec 2007, ZS Saad, ConvertDset, level 2 (MINOR), type 0 (GENERAL)
Output of full dsets if needed
This can be used to force a dataset with data
defined on a few nodes to be written out with a
complete list of nodes, using 0 where no data are defined.
06 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add -jpg and -png options to 1dplot.c.
* Add thick line drawing to mri_coxplot.c (by repeated thin line drawing).
03 Dec 2007, RC Reynolds, GIFTI, level 3 (MAJOR), type 0 (GENERAL)
initial release of gifti I/O C API
auto-generated by afni_history on Nov 24 2009