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) ---- 28 Aug 2019, P Taylor, lib_gershgorin.py, level 2 (MINOR), type 1 (NEW_PROG) Funcs to answer question: is this aff12 matrix very different from I? Uses fun algebraic facts known to and shared by the inimitable RWC.
15 Aug 2019, DR Glen, @animal_warper, level 3 (MAJOR), type 1 (NEW_PROG) Warp data to template and atlas segmentation to subject Tested for macaques. Derived from macaque_align.csh and NMT_subject_align.csh
25 Jul 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 1 (NEW_PROG) Program to apply freq volume to EPI for B0 distortion correction. An honor to translate this program from one by Vinai Roopchansingh!
01 Jul 2019, P Taylor, dsetstat2p, level 1 (MICRO), type 1 (NEW_PROG) Complement of p2dsetstat. Convenience tool for converting a dset's stat to a p-value. 01 Jul 2019, P Taylor, @djunct_glue_imgs_vert, level 1 (MICRO), type 1 (NEW_PROG) New prog for APQC HTML stuff. Glue two images together vertically. Used when pixel x-dimensions match (mainly for APQC HTML).
19 Jun 2019, P Taylor, @djunct_make_script_and_rst.py, level 1 (MICRO), type 1 (NEW_PROG) New prog for Sphinx doc generation (well, assistance). Somewhat simple markup scheme used to generate RST, images and scripts.
22 May 2019, P Taylor, @djunct_json_value.py, level 2 (MINOR), type 1 (NEW_PROG) Tiny program to extract values from JSONs. Just used by apqc_make_tcsh.py.
13 May 2019, DR Glen, 3dExchange, level 2 (MINOR), type 1 (NEW_PROG) Exchange specified values in a dataset Takes two columns of numbers to map input to output
22 Apr 2019, RW Cox, 1dApar2mat, level 1 (MICRO), type 1 (NEW_PROG) Compute the affine matrix from the parameters from 3dAllineate
29 Mar 2019, RW Cox, afni_check_omp, level 1 (MICRO), type 1 (NEW_PROG) Prints to stdout the number of OpenMP threads it detects For use in scripts, such as @SSwarper. This is a very short program.
07 Feb 2019, RC Reynolds, demoExpt.py, level 2 (MINOR), type 1 (NEW_PROG) will now actually distribute Vinai's demoExpt.py and afniInterfaceRT
03 Jan 2019, RW Cox, @afni_refacer_XXX, level 2 (MINOR), type 1 (NEW_PROG) Scripts to re-face a T1-weighted dataset @afni_refacer_make_master = makes the 'shell' dataset used to replace the face @afni_refacer_run = runs re-facing on one input dataset
13 Dec 2018, RC Reynolds, @strip.whitespace, level 2 (MINOR), type 1 (NEW_PROG) stored under scripts_src; guess what it does
03 Dec 2018, RC Reynolds, test.afni.prog.help, level 2 (MINOR), type 1 (NEW_PROG) test running -help on AFNI programs This is a build tool, not for the distribution.
20 Nov 2018, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 1 (NEW_PROG) For use with @chauffeur_afni: subroutine that used to be *in* it. More modular and useful now, better selection of montage xhair loc, too.
01 Nov 2018, P Taylor, 1dplot.py, level 3 (MAJOR), type 1 (NEW_PROG) New plotting program for 1D files. Copies much of the fun 1dplot capability to some pythonic realm.
21 Oct 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 1 (NEW_PROG) Helper program for afni_proc.py. Make @ss_review_html script for HTML version of AP QC. 21 Oct 2018, P Taylor, apqc_make_html.py, level 2 (MINOR), type 1 (NEW_PROG) Helper program for afni_proc.py. Run @ss_review_html, build QC dir with html file for ss review.
15 Oct 2018, P Taylor, @djunct_slice_space, level 2 (MINOR), type 1 (NEW_PROG) Helper program for @chauffeur_afni. Calculate even spacing of slices for montaging. 15 Oct 2018, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 1 (NEW_PROG) Helper program for @chauffeur_afni-- wrapper of it for QC stuff. It's for alignment checking, and it's... edgy.
28 Aug 2018, P Taylor, @xyz_to_ijk, level 2 (MINOR), type 1 (NEW_PROG) Helper program to be able to convert xyz coors to ijk indices. Supplementary program.
23 Aug 2018, RW Cox, 1dsound, level 2 (MINOR), type 1 (NEW_PROG) program to generate .au sound file from a 1D file Very primitive at this moment.
21 Jun 2018, RC Reynolds, model_PRF_6_BAD, level 2 (MINOR), type 1 (NEW_PROG) old model_PRF_6, but with version and gauss_file udpates This is for result comparison. 21 Jun 2018, RC Reynolds, get_afni_model_PRF_6_BAD, level 1 (MICRO), type 1 (NEW_PROG) wrapper for model Conv_PRF_6_BAD See model Conv_PRF_6_BAD in model_conv_PRF_6_BAD.c.
23 May 2018, RC Reynolds, get_afni_model_PRF_6, level 2 (MINOR), type 1 (NEW_PROG) this is just a wrapper for model parameter evaluation See model Conv_PRF_6 in model_conv_PRF_6.c. 23 May 2018, RC Reynolds, get_afni_model_PRF, level 2 (MINOR), type 1 (NEW_PROG) this is just a wrapper for model parameter evaluation See model Conv_PRF in model_conv_PRF.c.
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.
14 May 2018, RC Reynolds, @stim_analyze_modern, level 2 (MINOR), type 1 (NEW_PROG) added this sample script to doc/misc_scripts This uses the advanced form of make_random_timing.py.
12 May 2018, P Taylor, 3dClusterize, level 3 (MAJOR), type 1 (NEW_PROG) Perform clusterizing (voxelwise and volume-wise thresholding) on a dset. Basically like 3dclust but has some new options and easier syntax.
07 May 2018, RW Cox, @grayplot, level 2 (MINOR), type 1 (NEW_PROG) Script to drive 3dGrayplot in afni_proc.py output directory Will grayplot errts* and all_runs datasets, with motion indicator graph and (if available) sum_ideal.1D graph.
04 May 2018, JK Rajendra, BayesianGroupAna.py, level 4 (SUPER), type 1 (NEW_PROG) New program to preform Bayesian group analysis on ROI level data.
03 May 2018, RC Reynolds, @extract_meica_ortvec, level 2 (MINOR), type 1 (NEW_PROG) new program to extract MEICA projection vectors These 'rejected' terms are orthogonalized to the 'accepted' ones. This was written to be called by afni_proc.py.
26 Apr 2018, DR Glen, @surf_to_vol_spackle, level 2 (MINOR), type 1 (NEW_PROG) propagate surface to volume and fill holes
22 Apr 2018, P Taylor, 3dSliceNDice, level 3 (MAJOR), type 1 (NEW_PROG) Calculate Dice coefficients between volumes on a slicewise basis. Useful for comparing masks/maps of volumes.
16 Apr 2018, P Taylor, p2dsetstat, level 3 (MAJOR), type 1 (NEW_PROG) Program to convert a p-value to a statistic, using params in dset header. Useful to calculate thresholds for a particular volume.
09 Apr 2018, RW Cox, 3dGrayplot, level 2 (MINOR), type 1 (NEW_PROG) A plot, a la JD Power, of time series intensities in a brain mask For Cesar Caballero-Gaudes, and anyone else who actually cares about data quality.
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
15 Feb 2018, RC Reynolds, @compute_OC_weights, level 3 (MAJOR), type 1 (NEW_PROG) compute voxelwise weights for optimally combining multi-echo data The equations are based on the summer 2017 talk by J Gonzalez-Castillo.
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
29 Nov 2017, P Taylor, @djunct_4d_imager, level 3 (MAJOR), type 1 (NEW_PROG) Helper function to make montages and movies of 4D dsets. Useful when proc'ing dsets, make record of them.
26 Oct 2017, P Taylor, fat_proc_connec_vis, level 3 (MAJOR), type 1 (NEW_PROG) Visualize 'white matter connection' volumes output by 3dTrackID. Combine separate '-dump_rois ...' output into SUMAble surface maps.
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
08 Aug 2017, P Taylor, @suma_reprefixize_spec, level 2 (MINOR), type 1 (NEW_PROG) Helper function to copy a spec file whilst renaming files inside. Useful when copying a lot of *.gii or other surface files.
02 Aug 2017, RW Cox, 3dBrainSync, level 3 (MAJOR), type 1 (NEW_PROG) BrainSync algorithm of Joshi, from OHBM 2017 Also, my own permutation method (to avoid linear combination of disparate time points).
19 Jul 2017, RC Reynolds, 3dTto1D, level 3 (MAJOR), type 1 (NEW_PROG) time series to 1D : e.g. compute enorm, DVARS(RMS), SRMS Given time series data such as EPI or motion parameters, compute things like Euclidean norm and RMS (a.k.a. DVARS).
10 May 2017, RC Reynolds, model_conv_PRF_DOG, level 2 (MINOR), type 1 (NEW_PROG) new model: same as PRF, but Difference of Gaussians For E Silson and C Baker.
29 Mar 2017, JK Rajendra, prompt_popup, level 2 (MINOR), type 1 (NEW_PROG) add new program prompt_popup Similar to prompt_user, but adds label customization and up to 3 buttons
28 Feb 2017, RW Cox, 3dExtractGroupInCorr, level 1 (MICRO), type 1 (NEW_PROG) Program to reconstruct individual dataset from a .niml/.data pair. This program is for any unfortunate person who has lost the datasets that were used to create the 3dGroupInCorr inputs. It is not really 'NEW', since it has been around for my personal use for a while, but now it is being included in the AFNI distribution for the masses to enjoy.
13 Feb 2017, RW Cox, 3dSharpen, level 1 (MICRO), type 1 (NEW_PROG) Sharpening filter in 3D
26 Jan 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 1 (NEW_PROG) Simplish function for driving AFNI to make images/montages. Based on @snapshot_volreg; mainly intended for my selfish use. 26 Jan 2017, P Taylor, 1dDW_Grad_o_Mat++, level 2 (MINOR), type 1 (NEW_PROG) New program for changing/reformatting grads and things. Better defaults and simpler than original 1dDW_Grad_o_Mat++.
30 Dec 2016, P Taylor, @SUMA_renumber_FS, level 2 (MINOR), type 1 (NEW_PROG) New program for renumbering FS output after @SUMA_Make_Spec_FS. Also conglomerates things into tissue maps.
29 Dec 2016, RW Cox, @SSwarper, level 2 (MINOR), type 1 (NEW_PROG) New script to combine skull stripping and nonlinear warping Uses partial warping to improve skull stripping, and then finishes the warping, producing outputs compatible for use with afni_proc.py -tlrc_NL_warped_dsets
08 Dec 2016, RC Reynolds, 3dTsplit4D, level 2 (MINOR), type 1 (NEW_PROG) program to break 4D dataset into a set of 3D ones Authored by P Molfese.
07 Nov 2016, RW Cox, 3dTfilter, level 2 (MINOR), type 1 (NEW_PROG) Platform for generic filtering of time series Right now, just for adaptive local mean filtering (generalized smoothing plus despiking).
12 Oct 2016, RC Reynolds, RetroTS.py, level 3 (MAJOR), type 1 (NEW_PROG) distribute RetroTS.py (RetroTS.m converted to python) This should behave almost exactly as the MATLAB version. See 'RetroTS.py -help' for details. Much thanks to J Zosky for this contribution!
05 Oct 2016, RC Reynolds, afni-general, level 3 (MAJOR), type 1 (NEW_PROG) update from C Craddock and dclark87 New Programs: 3dLFCD, 3dDegreeCentrality, 3dECM, 3dMSE, 3dsvm_linpredict.
31 Aug 2016, P Taylor, 3dSpaceTimeCorr, level 3 (MAJOR), type 1 (NEW_PROG) New function for calculating spatial corr of temporal corr maps. Calc spatial corr of WB/mask connectivity maps; useful for RSFC?
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. 30 Aug 2016, RW Cox, 3dtoXdataset, level 2 (MINOR), type 1 (NEW_PROG) Convert 3D datasets to a list of in-mask shorts Purpose = compression for use in 3dClustSimX simulations. The '.sdat' format is now directly write-able from 3dttest++, so this program is probably not generally useful.
21 Jun 2016, P Taylor, @fat_tract_colorize, level 3 (MAJOR), type 1 (NEW_PROG) New function for coloring the volumetric tracking outputs. RGB coloration of local diffusion, esp. for PROB track output.
14 Jun 2016, P Taylor, 3dAmptoRSFC, level 3 (MAJOR), type 1 (NEW_PROG) New function for calculating RSFC params from one-side spectra. Complements 3dLombScargle. What an epithet.
09 Jun 2016, RW Cox, 3dLocalACF, level 2 (MINOR), type 1 (NEW_PROG) Estimate ACF parameters locally. Slow and experimental.
23 May 2016, RC Reynolds, parse_fs_lt_log.py, level 2 (MINOR), type 1 (NEW_PROG) get an index list from a FreeSurfer labletable log file
12 May 2016, P Taylor, 3dLombScargle, level 3 (MAJOR), type 1 (NEW_PROG) New function for calculating LS (normalized) periodogram from time series. Calculate magnitude spectrum from non-equisampled data.
19 Apr 2016, DR Glen, unWarpEPI.py, level 2 (MINOR), type 1 (NEW_PROG) blip-up/down distortion correction script
01 Mar 2016, RC Reynolds, tokens, level 2 (MINOR), type 1 (NEW_PROG) program to extract valid text entries from a file
26 Jan 2016, RW Cox, 1dNLfit, level 2 (MINOR), type 1 (NEW_PROG) 1D file nonlinear fitting Uses the 'calc' parser to define the function to fit. Mostly for the convenience of The Bob.
05 Jan 2016, RW Cox, @get.afni.version, level 1 (MICRO), type 1 (NEW_PROG) Script to fetch source for a particular AFNI version tag 05 Jan 2016, P Taylor, 3dVecRGB_to_HSL, level 3 (MAJOR), type 1 (NEW_PROG) Take a 3-vec to a single index on RGB color scale, and glue FA brick. Replaces earlier version, 3dVec_to_RGBind.
17 Dec 2015, RW Cox, stimband, level 1 (MICRO), type 1 (NEW_PROG) Computes freq band for stimuli extracted from .xmat.1D files For use in scripting bandwidths for pre- and post-processing.
16 Dec 2015, P Taylor, 3ddot_beta, level 3 (MAJOR), type 1 (NEW_PROG) Copy calc of 3ddot-- uses same functions-- just faster. Right now, can only calculate eta2; was asked for by user.
10 Nov 2015, P Taylor, 3dVec_to_RGBind.c, level 3 (MAJOR), type 1 (NEW_PROG) Take a 3-vec to a single index on RGB color scale, and glue FA brick. This will be useful in prob tract result plotting... script to come.
30 Oct 2015, RW Cox, images_equal, level 1 (MICRO), type 1 (NEW_PROG) Tests if 2 input 2D image files are equal.
16 Sep 2015, P Taylor, @GradFlipTest, level 3 (MAJOR), type 1 (NEW_PROG) For DWI analysis: test whether grads need to be flipped. Use a few tracking calls to estimate 'best' grad orientations.
21 Aug 2015, RC Reynolds, cifti_tool, level 3 (MAJOR), type 1 (NEW_PROG) initial release: updated help and added -hist New program to evaluate CIFTI datasets.
13 Jul 2015, RC Reynolds, nifti1_tool, level 2 (MINOR), type 1 (NEW_PROG) nifti1_tool is the NIFTI-1 version of nifti_tool
26 Jun 2015, RW Cox, 3dPval, level 1 (MICRO), type 1 (NEW_PROG) 3dPval converts statistics bricks to p-values For Isaac. Non-statistic bricks are converted to float and passed through unchanged.
10 Jun 2015, RC Reynolds, @diff.tree, level 3 (MAJOR), type 1 (NEW_PROG) look for differences between files in two directories Should merge @diff.files and @diff.tree, and change to python. 10 Jun 2015, RC Reynolds, @diff.files, level 3 (MAJOR), type 1 (NEW_PROG) compare list of files with those in other directory
04 May 2015, RW Cox, GLTsymtest, level 2 (MINOR), type 1 (NEW_PROG) For testing symbolic GLTs in a script So that the big boy (3dDeconvolve) doesn't have to be run just for this purpose. To help out with afni_proc.py
28 Apr 2015, RC Reynolds, clib_02.nifti2, level 2 (MINOR), type 1 (NEW_PROG) added clib_02.nifti2.c demo and Makefile under nifti2 dir
05 Feb 2015, ZS Saad, @Test_disk_IO, level 1 (MICRO), type 1 (NEW_PROG) Script to test disk I/O speeds
15 Jan 2015, RC Reynolds, afni_skeleton.py, level 1 (MICRO), type 1 (NEW_PROG) just to save a starting point for other new programs
14 Jan 2015, RC Reynolds, read_matlab_files.py, level 2 (MINOR), type 1 (NEW_PROG) read and possibly convert MATLAB files to 1D format
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.
18 Nov 2014, RW Cox, 3dTRfix, level 2 (MINOR), type 1 (NEW_PROG) Interpolate from a variable TR grid to a fixed TR grid For Javier et alii. No T1 artifact correction, just interpolation.
07 Nov 2014, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 1 (NEW_PROG) 6 parameter population receptive field estimate model Added sigrat (sigma ratio) and theta parameters. For E Silson and C Baker.
03 Nov 2014, G Chen, rPkgsInstall, level 2 (MINOR), type 1 (NEW_PROG) Install/check/update/remove R packages on the terminal This is an R program that allows the user to install, check, update, or remove R packages on the shell terminal.
19 Sep 2014, RC Reynolds, 3dexample1, level 2 (MINOR), type 1 (NEW_PROG) sample program to multiply a dataset by 2 This is very basic example of reading/processing/writing AFNI datasets.
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 specificies 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.
01 Aug 2014, ZS Saad, 3dGenFeatureDist, level 2 (MINOR), type 1 (NEW_PROG) Program written a while ago, placed in the distribution now
02 Jul 2014, RW Cox, 3dNwarpXYZ, level 2 (MINOR), type 1 (NEW_PROG) Nonlinear transform of xyz coordinate triples -- for Ziad
27 Jun 2014, RC Reynolds, model_conv_PRF, level 3 (MAJOR), type 1 (NEW_PROG) population receptive field estimate model For E Silson and C Baker.
19 Jun 2014, RW Cox, @Install_ClustScat_Demo, level 2 (MINOR), type 1 (NEW_PROG) Installs demo for Clusterize scatter plotting
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.
16 Apr 2014, ZS Saad, 3dRprogDemo, level 2 (MINOR), type 1 (NEW_PROG) A toy program to show how to write a command line R program with AFNI Created to help Cesar Caballero and Natalia Petridou implement their Paradigm Free Mapping method.
09 Apr 2014, RC Reynolds, gen_ss_review_table.py, level 3 (MAJOR), type 1 (NEW_PROG) parse output from @ss_review_basic text into spreadsheet format This makes it easy to flag outlier subject values. Thanks to J Jarcho for encouragement.
12 Mar 2014, ZS Saad, afni_open, level 2 (MINOR), type 1 (NEW_PROG) A simple program to help us open certain files on typical machines There is no help for the program yet, it is also not part of the compiled binaries yet. New functions such as GetAfniWebDownloader(), GetAfniPDFViewer(), and GetAfniImageViewer() were added to machdep.c
06 Mar 2014, P Taylor, 1dDW_Grad_o_Mat, level 3 (MAJOR), type 1 (NEW_PROG) Manipulate gradient/bmatrix files. Convert row/col and grad/bmatrix/gmatrix, use bval info, filter or not.
24 Dec 2013, ZS Saad, InstaTract, level 2 (MINOR), type 1 (NEW_PROG) Wrote the outlines of InstaTract to eventually perform miniprob tracking The program now talks to SUMA and receives queries from it. The queries return a dummy network for now. PT will make it interface with FATCAT to compute the actual tracts.
04 Dec 2013, RC Reynolds, afni_runme, level 2 (MINOR), type 1 (NEW_PROG) added this (Ziad's) script to sysadmin/scripts
13 Sep 2013, ZS Saad, 3dToyProg, level 1 (MICRO), type 1 (NEW_PROG) A sample program to illustrate I/O API for intrepid C programmers
11 Sep 2013, RC Reynolds, model_conv_cosine4, level 3 (MAJOR), type 1 (NEW_PROG) A four half-cosine convolvable model. Based on: Fully Bayesian Spatio-Temporal Modeling of FMRI Data IEEE Transactions on Medical Imaging, Volume 23, Issue 2, February 2004, Pages 213-231 Woolrich, M.W., Jenkinson, M., Brady, J.M., Smith, S.M. Requested by C Connolly and Felix.
09 Aug 2013, RW Cox, 3dTproject, level 2 (MINOR), type 1 (NEW_PROG) Rapid orthogonal projection to remove unwanted time series To replace 3dBandpass when necessary
26 Jul 2013, RW Cox, 3dNwarpFuncs, level 2 (MINOR), type 1 (NEW_PROG) Calculate various functions of a warp (e.g., Jacobian)
11 Jul 2013, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 1 (NEW_PROG) perform many checks to validate a system for AFNI use
07 Jul 2013, RC Reynolds, @Install_FATCAT_DEMO, level 2 (MINOR), type 1 (NEW_PROG) replaces @Install_PTaylor_TractDemo
31 May 2013, RC Reynolds, @simulate_motion, level 3 (MAJOR), type 1 (NEW_PROG) program to create time series simulated by motion parameters
24 Apr 2013, RC Reynolds, @move.to.series.dirs, level 2 (MINOR), type 1 (NEW_PROG) partition a list of DICOM files by series number Done for I Shapira.
22 Apr 2013, RW Cox, 3dNwarpAdjust, level 2 (MINOR), type 1 (NEW_PROG) For template-building via @toMNI_Qwarp Computes the mean warp, and adjusts the individual warps to get rid of this mean warp (under the presumption that it is some kind of bias).
12 Apr 2013, RW Cox, 3dLocalHistog, level 2 (MINOR), type 1 (NEW_PROG) Collecting counts of labels in nbhd of each voxel For building atlases that allow for uncertainty in position
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.
20 Feb 2013, RW Cox, 3dUnifize, level 2 (MINOR), type 1 (NEW_PROG) Quick and dirty approximate spatial uniformization of T1 anats Mostly for use with 3dQwarp
13 Feb 2013, RC Reynolds, unix_tutorial, level 3 (MAJOR), type 1 (NEW_PROG) added tutorial to CVS tree, with processed files under AFNI_data6
22 Jan 2013, ZS Saad, HalloSuma, level 2 (MINOR), type 1 (NEW_PROG) A sample light-weight program to illustrate 2-way communication with AFNI The program can be compiled in C or C++ along with the NIML library without having to link to AFNI/SUMA libraries. Documentation is the code.
18 Jan 2013, RC Reynolds, @compute_gcor, level 2 (MINOR), type 1 (NEW_PROG) compute GCOR = global correlation of a dataset
19 Oct 2012, G Chen, 3dMVM, level 3 (MAJOR), type 1 (NEW_PROG) Multivariate modeling approach to group analysis This is an R program that performs conventional ANOVA or ANCOVA-type analysis with no limit on the number of variables. See more details at https://afni.nimh.nih.gov/sscc/gangc/MVM.html
13 Oct 2012, ZS Saad, 3dHist, level 2 (MINOR), type 1 (NEW_PROG) Computes histograms using functions from the segmentation routines The program uses heuristics to automatically select histogram parameters, and it allows histogram queries. It had to be separate from 3dhistog because it uses libSUMA.a and because the latter's interface was getting too complicated.
28 Sep 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG) Added Paul Taylor's map_TrackID to warp tracks by an affine transform 28 Sep 2012, ZS Saad, @T1scale, level 2 (MINOR), type 1 (NEW_PROG) A mini script to scale T1s by PD volumes Script uses method borrowed from @CalculateSignatures to reduce bias field in T1 using a PD volume. Script also works well without PD.
18 Sep 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG) Checked in Prantik Kundu's MEICA tools. Try meica.py -help, also try @Install_MEICA_Demo
24 Aug 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG) Added Paul Taylor's 3dRSFC to the distribution 24 Aug 2012, ZS Saad, niprobe, level 1 (MICRO), type 1 (NEW_PROG) A variant on niccc to handle certain NIML file probing operations 24 Aug 2012, RC Reynolds, column_cat, level 3 (MAJOR), type 1 (NEW_PROG) like 'cat', except horizontally (see recent Unix command, 'paste')
03 Aug 2012, RW Cox, 2perm, level 1 (MICRO), type 1 (NEW_PROG) For generating 2 random subsets of a sequence of integers
18 Jul 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG) Added Paul Taylor's 3dReHo to the distribution
29 Jun 2012, RC Reynolds, @Install_RSFMRI_Motion_Group_Demo, level 2 (MINOR), type 1 (NEW_PROG) program is for installing demo of RSFMR on big and small motion groups
04 Jun 2012, ZS Saad, @Install_TSrestMovieDemo, level 1 (MICRO), type 1 (NEW_PROG) Demo script to make a resting state movie a la Daniel Margulies' 04 Jun 2012, ZS Saad, @Install_AfniRetinoDemo, level 1 (MICRO), type 1 (NEW_PROG) Demo script to download and run Retinotopy pipeline demo
07 May 2012, RW Cox, FIRdesign, level 1 (MICRO), type 1 (NEW_PROG) Finite Impulse Design filter design program -- for bandpass
30 Apr 2012, RC Reynolds, afni_restproc.py, level 3 (MAJOR), type 1 (NEW_PROG) this program is by Rayus Kuplicki, please contact him for information
27 Apr 2012, RC Reynolds, 3dmask_tool, level 3 (MAJOR), type 1 (NEW_PROG) a program to manipulate mask datasets
05 Apr 2012, RW Cox, 3dTnorm, level 2 (MINOR), type 1 (NEW_PROG) Normalize each time series in a dataset Like 1dnorm for 3D+time datasets
06 Mar 2012, RW Cox, 3dNormalityTest, level 2 (MINOR), type 1 (NEW_PROG) Test voxel values for normality (Gaussianity). Uses the Anderson-Darling test.
26 Jan 2012, ZS Saad, 3dinfill, level 2 (MINOR), type 1 (NEW_PROG) Fills holes in a volume based on neighboring values This program is a wrapper to function SUMA_VolumeInFill. Written in response to a query by Mike Beauchamp.
24 Jan 2012, ZS Saad, SurfExtrema, level 2 (MINOR), type 1 (NEW_PROG) Finds nodes that are local extrema on the surface. Program in response to request by Daniel Margulies
10 Jan 2012, RW Cox, 1dBport, level 2 (MINOR), type 1 (NEW_PROG) Generates sin/cos waveforms for bandpass-via-regression
30 Dec 2011, ZS Saad, @Atlasize, level 2 (MINOR), type 1 (NEW_PROG) A convenience script to turn a dataset to an atlas The script makes it easy to create a group atlas or a single-subject atlas and place them automatically in a location that AFNI recognizes making them available to the user without bothering with too many environment variable settings. 30 Dec 2011, ZS Saad, @AfniEnv, level 2 (MINOR), type 1 (NEW_PROG) A convenience script to automatically edit .afnirc
22 Dec 2011, RW Cox, mycat, level 1 (MICRO), type 1 (NEW_PROG) Minor program to be sort of like 'cat' but un-Microsofts files.
15 Dec 2011, RW Cox, 3dLSS, level 1 (MICRO), type 1 (NEW_PROG) 3dLSS implement LS-S regression As described in Mumford, Turner, Asby, and Poldrack, NeuroImage 2011. See 3dLSS -help for more info.
12 Dec 2011, ZS Saad, @global_parse, level 2 (MINOR), type 1 (NEW_PROG) Script to simplify support of global options such as h_find from scripts
29 Nov 2011, ZS Saad, @clean_help_dir, level 1 (MICRO), type 1 (NEW_PROG) Removes redundant help files from the afni help directory. 29 Nov 2011, ZS Saad, @DeblankFileNames, level 1 (MICRO), type 1 (NEW_PROG) Replaces spaces in filenames with_something_less_annoying.
21 Nov 2011, RC Reynolds, quick.alpha.vals.py, level 2 (MINOR), type 1 (NEW_PROG) a very simple program to tabulate the output from slow_surf_clustsim.py This ought to be improved, but at least it is now distributed...
17 Nov 2011, ZS Saad, apsearch, level 2 (MINOR), type 1 (NEW_PROG) This is a program to test approximate string matching functions The program is best described by its help output. It is meant to quickly test the behavior of the approx* functions in thd_ttatlas_query.c where approximate string matching will be useful is easily specifying an atlas areas by name. Another useful offshoot is the function: suggest_best_prog_option which can easily be called right after a command-line parsing error message is displayed. For example, in apsearch I have the following: { /* bad news in tennis shoes */ fprintf(stderr,"** Error %s: bad option %s\n", argv[0], argv[iarg]); suggest_best_prog_option(argv[0], argv[iarg]); return 1; } So all is needed to retrofit an old program is the suggest function. That function will do nothing if environment variable AFNI_NO_OPTION_HINT is set. To use suggest_best_prog_option from a script, use: apsearch -popt `basnemane $0` -word ARG
15 Nov 2011, RW Cox, dicom_hinfo, level 2 (MINOR), type 1 (NEW_PROG) For printing out info from lots of DICOM files For each file input, prints 1 line with the values of only the desired tags. The goal is to be helpful in figuring out which files go together. See Example #2 in the help output for such a case.
22 Sep 2011, RC Reynolds, uber_ttest.py, level 3 (MAJOR), type 1 (NEW_PROG) a graphical program for running either 3dttest++ or 3dMEMA Still under destruction.
01 Sep 2011, RC Reynolds, @radial_correlate, level 2 (MINOR), type 1 (NEW_PROG) compute voxelwise EPI correlations with local spherical averages
09 Aug 2011, RW Cox, 3dNwarpCalc, level 2 (MINOR), type 1 (NEW_PROG) Implemented about 80% of it Seems to work, but needs a fair amount of fine tuning and testing.
20 Jul 2011, RC Reynolds, make_pq_script.py, level 2 (MINOR), type 1 (NEW_PROG) program will generate a script to produce a p-value/q-value curve pair
11 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 3 (MAJOR), type 1 (NEW_PROG) for generating single subject review scripts To be run by the afni_proc.py proc script or directly by users.
24 Jun 2011, RC Reynolds, slow_surf_clustsim.py, level 3 (MAJOR), type 1 (NEW_PROG) a temporary program until we do this in C
08 Jun 2011, ZS Saad, @FSlabel2dset, level 2 (MINOR), type 1 (NEW_PROG) Script to change FreeSurfer ascii label file to SUMA dset
25 May 2011, RW Cox, @1dDiffMag, level 1 (MICRO), type 1 (NEW_PROG) Computes magnitude of 1st differences of 1D file
19 May 2011, RW Cox, 1dCorrelate, level 2 (MINOR), type 1 (NEW_PROG) Compute correlation coefficients of 1D columns Pearson, Spearman, Quadrant, or Kendall tau_b. Main goal is to provide the bias-corrected bootstrap estimate of the 95% confidence interval.
12 May 2011, RC Reynolds, uber_skel.py, level 3 (MAJOR), type 1 (NEW_PROG) A working skeleton for future uber programs. This is based on uber_align_test.py, version 0.2.
28 Apr 2011, RC Reynolds, uber_align_test.py, level 3 (MAJOR), type 1 (NEW_PROG) for testing EPI/anat alignment with various align_epi_anat.py options This is a command-line version, with a GUI to come soon.
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.
30 Dec 2010, RW Cox, 3dApplyNwarp, level 2 (MINOR), type 1 (NEW_PROG) Applies -nwarp_save output from 3dAllineate Lets you apply a 3D nonlinear deformation to another file. Works OK, but changes will come.
23 Dec 2010, RW Cox, 3dPolyfit, level 2 (MINOR), type 1 (NEW_PROG) Fits a polynomial (spatially) to a dataset
21 Dec 2010, ZS Saad, @help.AFNI, level 2 (MINOR), type 1 (NEW_PROG) A simple script to look at AFNI's all help page
08 Dec 2010, RW Cox, 3dXYZcat, level 2 (MINOR), type 1 (NEW_PROG) Generalized 3dZcat. No generalized 3dZcutup yet, though.
05 Nov 2010, ZS Saad, 3dkmeans, level 3 (MAJOR), type 1 (NEW_PROG) 3dkmeans is a program for performing kmeans clustering Program was written by A. Vovk and Z. Saad, based on The C clustering library. Copyright (C) 2002 Michiel Jan Laurens de Hoon. See suma -sources for copyright details See 3dkmeans -help for usage details.
29 Oct 2010, ZS Saad, @ElectroGrid, level 2 (MINOR), type 1 (NEW_PROG) A script for facilitating ECOG grid creation
28 Oct 2010, ZS Saad, @RegroupLabels, level 2 (MINOR), type 1 (NEW_PROG) A script for regrouping label datasets
25 Oct 2010, RC Reynolds, gen_group_command.py, level 3 (MAJOR), type 1 (NEW_PROG) a program to generate group commands (3dMEMA for now) Commands to come: 3dttest(++), 3dANOVA*, GroupANA.
20 Oct 2010, ZS Saad, niccc, level 1 (MICRO), type 1 (NEW_PROG) Started making niccc as part of the default compilation The program, originally written by Bob, is useful for testing NIML functions
12 Oct 2010, DR Glen, 3dDTtoDWI, level 2 (MINOR), type 1 (NEW_PROG) Program to compute DWI images from diffusion tensor Release from old code, bug fix for scale factors and lower triangular order.
29 Sep 2010, G Chen, 1dSVAR.R, level 3 (MAJOR), type 1 (NEW_PROG) Structural vector autoregression (SVAR) This is an R program that incorporates both instantaneous and lagged effects in an SVAR model for ROI-based network analysis. See more details at https://afni.nimh.nih.gov/sscc/gangc/SVAR.html
23 Aug 2010, ZS Saad, SurfRetinoMap, level 3 (MAJOR), type 1 (NEW_PROG) Calculates Visual Field Signs from visual field angle data 23 Aug 2010, ZS Saad, @RetinoProc, level 3 (MAJOR), type 1 (NEW_PROG) Packages processing step for phase-based retinotopic mapping. See @RetinoProc -help for details 23 Aug 2010, ZS Saad, 3dRetinoPhase, level 3 (MAJOR), type 1 (NEW_PROG) Calculate visual field angle from phase-based retinotopy data.
29 Jul 2010, RW Cox, 3dttest_new, level 3 (MAJOR), type 1 (NEW_PROG) New and improved version of 3dttest! With covariates, including per-voxel covariates! It slices, it dices! But wait, there's more! For no extra charge, it masks!
08 Jul 2010, G Chen, 3dICC_REML.R, level 2 (MINOR), type 1 (NEW_PROG) IntraClass Correlation (ICC) with REML Method This is an R program that calculates ICC with REML method on 3D volume data based on linear mixed-effects modeling scheme. See more details at https://afni.nimh.nih.gov/sscc/gangc/ICC_REML.html
07 Jul 2010, RW Cox, 3dClustSim, level 3 (MAJOR), type 1 (NEW_PROG) Like AlphaSim, but faster and terser output Computes C(p,a) = cluster size threshold for a range of p and a values: p = per-voxel (uncorrected) threshold p-value a = corrected probability level desired = probability of at least one noise-only cluster happening when the cluster size threshold is C(p,a) Optimized to use OpenMP for speed.
18 Jun 2010, RW Cox, 3dSimARMA11, level 1 (MICRO), type 1 (NEW_PROG) Simulating ARMA(1,1) time series for testing 3dREMLfit + 3dMEMA
30 Apr 2010, RW Cox, 3dTcorr1D, level 2 (MINOR), type 1 (NEW_PROG) Like 3dTcorrelate, but between a 1D file and a 3D+time dataset Really a very simple program, with 4 options for the 'correlation' coefficient computation: Pearson, Spearman, Quadrant, and Kendall tau_b.
08 Feb 2010, RW Cox, 3dSatCheck, level 1 (MICRO), type 1 (NEW_PROG) Program to check for initial transients i.e., if the FMRI time series has non-saturated time points at the beginning (on average) -- uses the code thd_satcheck.c for the real work -- the same as used in 3dBandpass. At this time, 3dSatCheck is not compiled in the binary distributions of AFNI.
31 Dec 2009, RW Cox, 3dGroupInCorr, level 3 (MAJOR), type 1 (NEW_PROG) Group InstaCorr With changes to afni and also new program 3dSetupGroupInCorr
18 Dec 2009, RW Cox, 3dBandpass, level 1 (MICRO), type 1 (NEW_PROG) Finally finished this!
03 Dec 2009, RW Cox, 3dLocalPV, level 2 (MINOR), type 1 (NEW_PROG) Speeded up version of 3dLocalSVD Speed comes with some small limitations. About 30% faster.
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_receiver.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.
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 https://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) with ANOVA scheme 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 https://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 https://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 https://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, ExamineXmat, 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 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.
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 https://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: https://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: 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
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 Oct 17 2019