AFNI HISTORY
level 4 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 4
---- log of AFNI updates (most recent first) ----
19 Feb 2019, P Taylor, apqc_make_tcsh.py, level 5 (SUPERDUPER), type 0 (GENERAL)
Much functionality changed/improved (hopefully).
More output, better formats, help and HTML framework.
19 Feb 2019, P Taylor, apqc_make_html.py, level 5 (SUPERDUPER), type 0 (GENERAL)
Much functionality changed/improved (hopefully).
More output, better formats, help and HTML framework.
18 May 2018, JK Rajendra, abids_tool.py, level 4 (SUPER), type 1 (NEW_PROG)
New program to modify BIDS datasets.
18 May 2018, JK Rajendra, abids_lib.py, level 4 (SUPER), type 1 (NEW_PROG)
New library to handle data from json files. Useful for BIDS data.
18 May 2018, JK Rajendra, abids_json_info.py, level 4 (SUPER), type 1 (NEW_PROG)
New program to extract data from json files. Useful for BIDS data.
04 May 2018, JK Rajendra, BayesianGroupAna.py, level 4 (SUPER), type 1 (NEW_PROG)
New program to perform Bayesian group analysis on ROI level data.
23 Mar 2018, JK Rajendra, tedana_wrapper.py, level 4 (SUPER), type 1 (NEW_PROG)
add wrapper for tedana.py that will be run from afni_proc.py
18 Jan 2018, DR Glen, thickness scripts, level 4 (SUPER), type 1 (NEW_PROG)
Scripts to compute thickness of a mask 3 ways
@measure_bb_thick, @measure_erosion_thick, @measure_in2out
Suite of thickness scripts to compute thickness in volume
and map to surface. Master script, @thickness_master, to
call others with option for FreeSurfer input data
25 Oct 2017, JK Rajendra, @afni_R_package_install, level 4 (SUPER), type 1 (NEW_PROG)
add new program @afni_R_package_install
Will install R libraries to run shiny apps
11 Oct 2017, JK Rajendra, ClustExp_StatParse.py, level 4 (SUPER), type 1 (NEW_PROG)
add new program ClustExp_StatParse.py
Part of cluster explorer. Extract subject level data from clusters and
output tables and a shiny app
11 Oct 2017, JK Rajendra, ClustExp_HistTable.py, level 4 (SUPER), type 1 (NEW_PROG)
add new program ClustExp_HistTable.py
Part of cluster explorer. Extract data tables from the history of datasets
11 Oct 2017, JK Rajendra, @FATCAT_heatmap_shiny, level 4 (SUPER), type 1 (NEW_PROG)
add new program @FATCAT_heatmap_shiny
Run a shiny app to view .netcc or .grid files
11 Oct 2017, JK Rajendra, @ClustExp_run_shiny, level 4 (SUPER), type 1 (NEW_PROG)
add new program @ClustExp_run_shiny
Part of cluster explorer. Run the shiny app output from ClustExp_StatParse
.py
11 Oct 2017, JK Rajendra, @ClustExp_CatLab, level 4 (SUPER), type 1 (NEW_PROG)
add new program @ClustExp_CatLab
Part of cluster explorer. Concatenates and labels input datasets
30 Aug 2016, RW Cox, 3dClustSimX, level 4 (SUPER), type 1 (NEW_PROG)
Generalized cluster simulation
Hopefully, the new way forward. Not ready for general users yet, but
getting there.
21 Dec 2014, P Taylor, fat_mat_sel.py, level 4 (SUPER), type 1 (NEW_PROG)
Plot, view and save matrix file info.
Works for both 3dNetCorr and 3dTrackID info.
08 Sep 2014, P Taylor, fat_roi_row.py, level 4 (SUPER), type 1 (NEW_PROG)
Select out one row of a matrix file, at user request.
Useful, for example, if wanting to view connectivity one-to-many.
08 Sep 2014, P Taylor, fat_mvm_scripter.py, level 4 (SUPER), type 1 (NEW_PROG)
Connect FATCAT with 3dMVM-- write a basic command call to 3dMVM.
User specifies specific model, and awaaaay we go.
08 Sep 2014, P Taylor, fat_mvm_prep.py, level 4 (SUPER), type 1 (NEW_PROG)
Connect FATCAT with 3dMVM-- combine CSV and matrix data.
Build data table necessary for 3dMVM from MRI+other data.
08 Sep 2014, P Taylor, fat_mvm_gridconv.py, level 4 (SUPER), type 1 (NEW_PROG)
Connect FATCAT with 3dMVM-- modernize format of old *.grid files.
Prehistoric grid files had no labels. This updates them.
21 Apr 2014, P Taylor, TORTOISEtoHere, level 4 (SUPER), type 1 (NEW_PROG)
New program: convert TORTOISE DTs to AFNI format.
This also allows flipping/rescaling to be done.
21 Apr 2014, P Taylor, 3dEigsToDT, level 4 (SUPER), type 1 (NEW_PROG)
New program: take in eigen{values,vectors} and calculate DT.
This also allows flipping/rescaling to be done.
06 Mar 2014, P Taylor, 3dTrackID, level 5 (SUPERDUPER), type 5 (MODIFY)
Have Cordelialy unified the three kingdoms of tracking, cLearing usage.
This program does all tracking, including HARDI and mini-probabilistic.
06 Mar 2014, P Taylor, 3dProbTrackID, level 5 (SUPERDUPER), type 5 (MODIFY)
Put out to pasture.
This program is now retired, with usage cleanly transferred to 3dTrackID.
14 Mar 2013, P Taylor, 3dNetCorr, level 4 (SUPER), type 1 (NEW_PROG)
New function: calculate correlat/Z of ROIs in a network.
This program works on several networks as separate subbricks simultan-
eously.
21 Feb 2012, DR Glen, whereami, level 4 (SUPER), type 2 (NEW_OPT)
Web-based access atlases available
Able to query web atlases from whereami and open webpages
Support starting with rat brain atlas from Elsevier's
BrainNavigator
10 Jun 2011, DR Glen, whereami, level 4 (SUPER), type 0 (GENERAL)
Generic Atlas Support and new atlases
Atlases, spaces and transformations are now defined in a NIML file,
AFNI_atlas_spaces.niml. Transformations among spaces for coordinates
are defined in that file for use by whereami and the whereami display
in the AFNI GUI. The flexible naming of the spaces and atlases allows
easy addition of new atlases to AFNI processing.
Two new environment variables control what atlases and spaces are shown
when no atlas is specified, AFNI_ATLAS_LIST and AFNI_TEMPLATE_SPACE_LIST
The list of atlases now defaults to the TT_Daemon and the Eickhoff-
Zilles atlases in MNI_ANAT space.
Additionally, the cytoarchitectonic atlases from the Zilles, Eickhoff
group have been updated to the most recent version, 1.8.
***The previous versions, 1.5, are not used in this release by default.
Depending upon differences on how regions or codes are defined and used,
it is possible that processing scripts and results may be affected.
With this release, we also introduce three probabilistic atlases
donated by the Desai group generated from a typical AFNI pipeline.
These atlases contain a multitude of regions created using both
@auto_tlrc and FreeSurfer.
15 Feb 2011, RC Reynolds, uber_subject.py, level 4 (SUPER), type 1 (NEW_PROG)
added CLI (command-line interface), generates basic afni_proc.py script
Many enhancements yet to come.
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 https://afni.nimh.nih.gov/sscc/gangc/MEMA.html
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.
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
https://afni.nimh.nih.gov/sscc/gangc/1dGC
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.
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.
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
https://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.
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.
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.
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 https://afni.nimh.nih.gov/sscc/gangc/lme.html
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: https://afni.nimh.nih.gov/sscc/gangc/PathAna.html
20 Dec 2006, RC Reynolds, afni_proc.py, level 4 (SUPER), type 1 (NEW_PROG)
program to write complete single subject FMRI processing script
03 Aug 2006, RC Reynolds, NI_SURF_DSET, level 4 (SUPER), type 0 (GENERAL)
added a new surface dataset format, with read/write ability in AFNI
02 Dec 2005, RC Reynolds, ANOVA, level 5 (SUPERDUPER), type 5 (MODIFY)
changed variance computations in 3dANOVA programs to not assume sphericity
For details, see https://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html .
23 Sep 2005, G Chen, 3dANOVA2 and 3dANOVA3, level 4 (SUPER), type 4 (BUG_FIX)
Significant modifications in 3dANOVA2 and 3dANOVA3
The changes were made to avoid statistics inflation for general linear
contrasts when coefficients don't add up to 0. See more details at
https://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html
05 Jul 2005, RC Reynolds, Dimon, level 4 (SUPER), type 1 (NEW_PROG)
program to monitor real-time acquisition of DICOM images
25 Apr 2005, RC Reynolds, NIFTI, level 4 (SUPER), type 0 (GENERAL)
AFNI can read and write NIFTI datasets (effort with Bob and Rich)
07 Jan 2005, RC Reynolds, nifti_tool, level 4 (SUPER), type 1 (NEW_PROG)
program to directly manipulate or compare NIFTI dataset headers
07 Jan 2005, RC Reynolds, NIFTI, level 4 (SUPER), type 0 (GENERAL)
initial release of NIFTI library
04 Oct 2004, RC Reynolds, vol2surf, level 4 (SUPER), type 0 (GENERAL)
added vol2surf interface for real-time mapping from afni to suma
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: https://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 https://afni.nimh.nih.gov/sscc/gangc
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
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
16 Jan 2001, RW Cox, AFNI-general, level 5 (SUPERDUPER), type 0 (GENERAL)
Older History stuff
===========================================================
== This was the day I (RWC) started working at the NIH! :) ==
== All changes from this date onwards were made at the NIH ==
===========================================================
24 Jul 1996, RW Cox, Miscellaneous, level 5 (SUPERDUPER), type 0 (GENERAL)
Oldest History stuff
AFNI was created in summer 1994 (but some parts date to the 1980s).
However, no formal log was made of changes until this date in 1996.
So this is the beginning of AFNI historiography.
'Lately it occurs to me: What a long, strange trip it's been.'
auto-generated by afni_history on Apr 18 2024