AFNI HISTORY
all levels
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 -type NEW_PROG
---- log of AFNI updates (most recent first) ----
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.
21 Oct 2009, RW Cox, 1dAstrip, level 1 (MICRO), type 1 (NEW_PROG)
To remove Alpha characters from 1D-like files.
For my own ill-conceived plans for global domination. Cheap and not
perfect.
08 Oct 2009, RW Cox, 3dPeriodogram, level 1 (MICRO), type 1 (NEW_PROG)
Does what it sound like, more or less, I hope.
02 Oct 2009, RW Cox, 1dgenARMA11, level 1 (MICRO), type 1 (NEW_PROG)
Generates ARMA(1,1) correlated noise time series
For simulation purposes.
29 Sep 2009, RC Reynolds, @Reorder, level 2 (MINOR), type 1 (NEW_PROG)
script version of reorder plugin, for J. Bjork
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
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.
16 Jul 2009, RC Reynolds, realtime_receiver.py, level 3 (MAJOR), type 1 (NEW_PROG)
replacement for serial_helper
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.
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.
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
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, @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.
30 Apr 2009, RW Cox, 1dBandpass, level 1 (MICRO), type 1 (NEW_PROG)
for .. Bandpassing!
Really just to test the new bandpassing functions for inclusion into
AFNI's InstaCorr feature.
04 Apr 2009, RW Cox, 3dmaskSVD, level 2 (MINOR), type 1 (NEW_PROG)
Like 3dmaskave, but does SVD principal vector instead of average
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.
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.
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
03 Mar 2009, RC Reynolds, @build.Xlib, level 2 (MINOR), type 1 (NEW_PROG)
this is a build script for the local X packages
13 Jan 2009, ZS Saad, afni-matlab, level 2 (MINOR), type 1 (NEW_PROG)
Added GS_orth_1D.m to perform Gram-Schmidt orthogonalization
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.
04 Dec 2008, RC Reynolds, balloon, level 1 (MICRO), type 1 (NEW_PROG)
new program by M Belmonte
02 Dec 2008, ZS Saad, SpharmReco, level 3 (MAJOR), type 1 (NEW_PROG)
Reconstructs data from spherical harmonics decomposition.
See SpharmDeco -help and the demo script @Spharm.examples
for details.
02 Dec 2008, ZS Saad, SpharmDeco, level 3 (MAJOR), type 1 (NEW_PROG)
Performs spherical harmonics decomposition.
This program performs spherical harmonics decomposition
for surfaces' geometry and/or surface-based data
See SpharmReco -help and the demo script @Spharm.examples
for details.
02 Dec 2008, ZS Saad, @Spharm.examples, level 3 (MAJOR), type 1 (NEW_PROG)
A script to demonstrate the usage of SpharmDeco and SpharmReco
02 Dec 2008, ZS Saad, @NoisySkullStrip, level 3 (MAJOR), type 1 (NEW_PROG)
A script to improve skull stripping in noisy of heavily shaded data
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.
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
14 Nov 2008, RW Cox, help_format, level 1 (MICRO), type 1 (NEW_PROG)
For formatting -help output into Web pages with hyperlinks.
To be used with the dist_help script for making the help Web pages from
the -help outputs of all AFNI programs.
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.
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.
15 Oct 2008, RW Cox, fdrval, level 2 (MINOR), type 1 (NEW_PROG)
Compute FDR value on command line, from dataset header
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
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).
29 Sep 2008, RC Reynolds, 3dmatmult, level 3 (MAJOR), type 1 (NEW_PROG)
program to multiply AFNI datasets slice-by-slice as matrices
29 Aug 2008, ZS Saad, ExamineXmatR, level 3 (MAJOR), type 1 (NEW_PROG)
An interactive tool to examine a design matrix
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!
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.
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.
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
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.
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'.
08 Apr 2008, RW Cox, 3dUpsample, level 2 (MINOR), type 1 (NEW_PROG)
Upsample a 3D+time dataset (in the time direction)
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.
01 Mar 2008, RW Cox, ++AFNI_History++ plugin, level 1 (MICRO), type 1 (NEW_PROG)
Provides a way to create and insert entries into afni_history_NAME.c
User must set two environment variables:
AFNI_HISTORY_PERSONAL_FILE = full path to your personal version of
afni_history_NAME.c
AFNI_HISTORY_USERNAME = what you want for the username in your file
My values of these are
AFNI_HISTORY_PERSONAL_FILE = /Users/rwcox/AFNI/src/afni_history_rwcox.c
AFNI_HISTORY_USERNAME = RWC
You also need to add one of two lines to your afni_history_NAME.c file:
/*=====below THIS LINE=====*/
or
/*=====above THIS LINE=====*/
as shown, with no blanks before or after on the same line (except that
you must make 'BELOW' or 'ABOVE' all caps!).
New history entries are placed below the 'BELOW' line (if present), or
above the 'ABOVE' line.
If you set AFNI_HISTORY_DONTSAVE to YES, then the afni_history_NAME.c
file won't be edited, and the new entry is just written to stdout.
29 Feb 2008, 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
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.
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.
06 Feb 2008, ZS Saad, SurfDist, level 3 (MAJOR), type 1 (NEW_PROG)
Program to calculate geodesic internodal distances
28 Dec 2007, RC Reynolds, gifti_tool, level 3 (MAJOR), type 1 (NEW_PROG)
program to read and write GIFTI datasets
18 Dec 2007, ZS Saad, ROIgrow, level 2 (MINOR), type 1 (NEW_PROG)
Grows regions separately, depending on labels
23 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 1 (NEW_PROG)
Older History stuff
* Modify NI_decode_one_string() in niml_elemio.c to auto-expand buffer
size if string is too long. For festering Lebanese programmers.
* Similarly, modify scan_for_angles() if element header is bigger than
buffer size.
* 'Histogram: Multi' (plug_histog_multi.c) plugin, for Kyle, Alex, & Pat.
20 Nov 2007, RW Cox, 3dTsort, level 3 (MAJOR), type 1 (NEW_PROG)
new program = sorts voxel data along the time axis
This might be useful for sorting the -stim_time_IM beta weights
output be 3dDeconvolve. Perhaps for something else, too?
20 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 1 (NEW_PROG)
Older History stuff
* Copy auxdata from source to output in 3dAllineate.c (oops).
* Changed 'report' from mri_clusterize.c and added info to the
clusterize vector chooser using about BHelp to see this report.
* New program 3dTsort.c. Will this grow to be a monster?
19 Nov 2007, ZS Saad, Surf2VolCoord, level 2 (MINOR), type 1 (NEW_PROG)
Program to show surface-node to voxel correspondence
This can be used to understand how surface coordinates
relate to voxel coordinates.
26 Sep 2007, ZS Saad, SurfFWHM, level 4 (SUPER), type 1 (NEW_PROG)
Program to estimate FWHM of data on surface
20 Sep 2007, G Chen, 3dLME.R, level 4 (SUPER), type 1 (NEW_PROG)
An R program for linear mixed-effects analysis at group level in AFNI
See more details at http://afni.nimh.nih.gov/sscc/gangc/lme.html
31 Aug 2007, RC Reynolds, model_conv_diffgamma, level 2 (MINOR), type 1 (NEW_PROG)
NLfim model to compute the convolution of the difference of gammas
05 Feb 2007, ZS Saad, SurfDsetInfo, level 2 (MINOR), type 1 (NEW_PROG)
Program to display surface dataset information
Output is crude at the moment.
17 Jan 2007, G Chen, 1dSEM, level 4 (SUPER), type 1 (NEW_PROG)
Path analysis (or structural equation modeling) at group level.
See more details on: http://afni.nimh.nih.gov/sscc/gangc/PathAna.html
05 Jan 2007, ZS Saad, imcat, level 2 (MINOR), type 1 (NEW_PROG)
Program to stitch images.
20 Dec 2006, RC Reynolds, afni_proc.py, level 4 (SUPER), type 1 (NEW_PROG)
program to write complete single subject FMRI processing script
11 Dec 2006, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 1 (NEW_PROG)
program to convert stim_files to stim_times files
22 Oct 2006, RC Reynolds, model_demri_3, level 3 (MAJOR), type 1 (NEW_PROG)
NLfim model for Dynamic Enhanced MRI
12 Oct 2006, RC Reynolds, serial_writer, level 2 (MINOR), type 1 (NEW_PROG)
program to send data from a file, pipe or made up to a given serial port
20 Sep 2006, ZS Saad, DriveSuma, level 3 (MAJOR), type 1 (NEW_PROG)
Program to control SUMA from the command line
31 Aug 2006, ZS Saad, AnalyzeTrace, level 1 (MICRO), type 1 (NEW_PROG)
Program to analyze the output of -trace option.
25 Jan 2006, RC Reynolds, model_michaelis_menton, level 3 (MAJOR), type 1 (NEW_PROG)
NLfim model function for ethanol studies
11 Oct 2005, RC Reynolds, 3dmaxima, level 3 (MAJOR), type 1 (NEW_PROG)
command-line version of maxima plugin
05 Jul 2005, RC Reynolds, Dimon, level 4 (SUPER), type 1 (NEW_PROG)
program to monitor real-time acquisition of DICOM images
07 Jan 2005, RC Reynolds, nifti_tool, level 4 (SUPER), type 1 (NEW_PROG)
program to directly manipulate or compare NIFTI dataset headers
27 Jul 2004, G Chen, PathAna, level 4 (SUPER), type 1 (NEW_PROG)
A Matlab package that runs group analysis of up to 5-way ANOVA
This package adopts the conventional ANOVA approach to handling gorup
analysis. And it requires Statistics Toolbox other than the basic Matlab.
See more details on: http://afni.nimh.nih.gov/sscc/gangc
27 Jul 2004, G Chen, IndiAna, level 4 (SUPER), type 1 (NEW_PROG)
A Matlab package for individual subject analysis
See more details at http://afni.nimh.nih.gov/sscc/gangc
31 Mar 2004, RC Reynolds, serial_helper, level 3 (MAJOR), type 1 (NEW_PROG)
program to pass realtime registration params from TCP to serial port
01 Dec 2003, RC Reynolds, SurfMeasures, level 3 (MAJOR), type 1 (NEW_PROG)
program to compute various measures over surfaces
05 Aug 2003, RC Reynolds, 3dVol2Surf, level 4 (SUPER), type 1 (NEW_PROG)
program to map data from the volume to domain to the surface domain
29 May 2003, RC Reynolds, 3dSurf2Vol, level 4 (SUPER), type 1 (NEW_PROG)
program to map data from the surface domain to the volume domain
27 Nov 2002, RC Reynolds, Imon, level 4 (SUPER), type 1 (NEW_PROG)
program to monitor GE I-files as they are written to the scanner
01 Oct 2002, RC Reynolds, file_tool, level 4 (SUPER), type 1 (NEW_PROG)
program to perform generic manipulations of binary files
20 Jun 2002, RC Reynolds, @make_stim_file, level 2 (MINOR), type 1 (NEW_PROG)
script to create binary stim files
06 Jun 2002, RC Reynolds, @SUMA_Make_Spec_FS, level 3 (MAJOR), type 1 (NEW_PROG)
script to import FreeSurfer surfaces into SUMA
21 May 2002, RC Reynolds, 3dresample, level 4 (SUPER), type 1 (NEW_PROG)
program to change a dataset orientation and/or grid spacing
08 Mar 2002, RC Reynolds, plug_crender, level 4 (SUPER), type 1 (NEW_PROG)
added rendering plugin to afni
auto-generated by afni_history on Nov 24 2009