AFNI HISTORY

level 3 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 3 -past_years 2 

---- log of AFNI updates (most recent first) ---- 20 Jul 2021, RW Cox, NIML library, level 3 (MAJOR), type 4 (BUG_FIX) NIML file: input failed if file over 2BG in size Due to storing filesize in int/long. Fix was to make it stored in int64_t, and fixing a few other places.
24 May 2021, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Several small updates for convenience and organization: help updated... more QC images; split intermediate text desc; new cmd_log.
17 May 2021, DR Glen, lesion_align, level 3 (MAJOR), type 1 (NEW_PROG) Alignment for data with large lesions Developed for hemispherectomy and lobectomy data. May be applicable to stroke and smaller lesion data too
06 Apr 2021, RC Reynolds, ap_run_simple_rest.tcsh, level 3 (MAJOR), type 1 (NEW_PROG) run a quick afni_proc.py resting state analysis for QC
24 Mar 2021, P Taylor, 3dBrickStat, level 3 (MAJOR), type 4 (BUG_FIX) Fix bug: having non-full-FOV mask + perc calcs affected other calcs. Calcs should now be consistent even with those opts used. Thanks, RCR.
27 Feb 2021, DR Glen, clang macos 11 M1-ARM mods, level 3 (MAJOR), type 0 (GENERAL) Makefile changes for ARM builds for new Macs Makefile, misc. changes for building for M1
07 Feb 2021, DR Glen, clang+gcc10 macos 10.15 mods, level 3 (MAJOR), type 4 (BUG_FIX) Lots of little code fixes to handle compiler warnings Makefile updated and some long outstanding issues fixed
19 Oct 2020, P Taylor, @djunct_overlap_check, level 3 (MAJOR), type 1 (NEW_PROG) Make of overlap of 2 datasets (esp for pre-align check, AW or SSW). Will make both non-obl and 3dWarp-deob'ed images of olap (and report). 19 Oct 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Simplifying output dir: Phase II and III. Thanks again, B Jung! New intermediate dir, animal_outs update, helpfile rewritten.
27 Aug 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 5 (MODIFY) Well, usage+output shouldn't really change, but it should be more stable. There is also a new opt: -align_centers_meth (read the help).
31 Jul 2020, P Taylor, @Install_MACAQUE_DEMO, level 3 (MAJOR), type 1 (NEW_PROG) Install MACAQUE_DEMO_REST_1.0, for macaque resting state FMRI examples. Has a '-lite_version' opt for truncated EPI version, smaller download.
30 Jul 2020, P Taylor, @Install_MACAQUE_DEMO, level 3 (MAJOR), type 0 (GENERAL) Now install MACAQUE_DEMO_2.1, which should be the new normal. Script checks for things on install, makes recs, more full demo.
01 Jul 2020, P Taylor, @Install_NMT, level 3 (MAJOR), type 1 (NEW_PROG) Installer for the NIMH Macaque Template(s) v2, and the CHARM (atlases). Courtesy of Ben Jung, Adam Messinger, et al.
10 Jun 2020, P Taylor, convert_cdiflist_to_grads.py, level 3 (MAJOR), type 1 (NEW_PROG) For GE scanners, we might want a cdiflist* file for DWI grad info. This prog converts such beasts into usable grad/bvalue files for proc.
03 Jun 2020, P Taylor, lib_mat2d_plot.py, level 3 (MAJOR), type 0 (GENERAL) Many updates to functioning, defaults, reading argv, applying user opts. Help file added as well; works with main proc: fat_mat2d_plot.py. 03 Jun 2020, P Taylor, fat_mat2d_plot.py, level 3 (MAJOR), type 1 (NEW_PROG) FINALLY, a python3 program to plot 3dTrackID and 3dNetCorr output. Plots *.grid and *.netcc files; replaces fat_mat_sel.py.
30 May 2020, P Taylor, @djunct_modal_smoothing_with_rep, level 3 (MAJOR), type 1 (NEW_PROG) Perform modal smoothing, and go back and add in any ROIs that were lost. May be useful in @animal_warper; may be good to add mask stuff, too. 30 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Default modal smoothing now is with replacement of any lost ROIs. Uses @djunct_modal* script; opt to not replace. More QC images now, too.
26 May 2020, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Two major changes in output: ve2a and LR-flipcheck now have EPI as ulay. Most anats are SSed, so better edges? Thanks for suggestion, O Esteban! 26 May 2020, P Taylor, @djunct_edgy_align_check, level 3 (MAJOR), type 0 (GENERAL) Several changes to make this appropriate using EPI as ulay. New opts, couple small bug fixes, couple tweaks.
21 May 2020, P Taylor, afni_seeds_per_space.txt, level 3 (MAJOR), type 0 (GENERAL) Keep up with change of macaque standard space naming: stereoNMT -> NMT2. 'stereoNMT' is an ex-parrot. 21 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 3 (MAJOR), type 1 (NEW_PROG) Adjunct program for @animal_warper.py; build ROI report table. Thanks to D Glen and A Messinger for helpful feedback+inputs. 21 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Add reports of warped and unwarped ROIs, via adjunct_aw_tableize*.py. Thanks to D Glen and A Messinger for helpful feedback+inputs.
18 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Large number of under-the-hood changes, as well as new opts. More general handling of followers and choosing file abbrevs.
12 Mar 2020, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 0 (GENERAL) This program has been deemed unnecessary. Thanks for the FS folks for discussions/clarifications on this.
10 Mar 2020, RW Cox, 3dttest++, level 3 (MAJOR), type 6 (ENHANCE) Add dataset-level weights to 3dttest++ Per the request of users in Tulsa. New options -setweight[AB] allow user to provide weights for the importance of a user in the calculations.
25 Feb 2020, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 0 (GENERAL) New min|max range on vox size; update report text. Based on tests with FS data.
19 Feb 2020, RC Reynolds, afni_python_wrapper.py, level 3 (MAJOR), type 1 (NEW_PROG) replaces afni_util.py as a main This program can theortically be used to call any AFNI python function from the shell.
12 Feb 2020, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) add ability to compare against examples Add options -compare_opts, -compare_example_pair, -show_example and -show_example_names. Consider these examples: afni_proc.py -show_example 'Example 11b' afni_proc.py -show_example_names afni_proc.py ... my options here ... -compare_opts 'Example 11' Motivated by C Gaillard and P Taylor.
27 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL) Program now outputs QC images automatically. These are output into a PREFIX_QC directory each run. 27 Jan 2020, P Taylor, @SSwarper, level 3 (MAJOR), type 0 (GENERAL) Large set of updates; many new opts added, too; generally much improved warps. Heavily tested on 178 subj across studies; output fnames are same, though.
26 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL) This program now requires specifying a mode for re/defacing. One can also output all types of re/defacing simultaneously.
24 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL) This program has been revamped and updated, including having a new ref vol. Syntax for running this has totally changed (options exist). 24 Jan 2020, P Taylor, @afni_refacer_make_master_addendum, level 3 (MAJOR), type 0 (GENERAL) This program just records additional tweaks to refacer ref vol. Not really meant to be run on its own; for future reference only.
22 Jan 2020, RW Cox, 3dREMLfit, level 3 (MAJOR), type 6 (ENHANCE) Compute Ljung-Box statistic for -Rvar dataset. Provides a measure of how temporally correlated each voxel's pre-whitened residuals are. Small LB value = good fit by the ARMA(1,1) model. Sub-brick is coded as a chi-squared statistic for use in thresholding in the AFNI GUI. 22 Jan 2020, RC Reynolds, plug_realtime, level 3 (MAJOR), type 0 (GENERAL) add ROIs and data mask method Added corresponding demo: AFNI_data6/realtime.demos/demo_3_ROIs_n_data
13 Jan 2020, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) New pieces of QC: first, seedbased corr maps for non-task data. Second, censor-based warnings (general and per-stim).
27 Dec 2019, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 2 (NEW_OPT) New option(s) to not just *check* a dset for FS-ability, but to correct it. The '-fix_all' and accompanying options control this. Bonne idee, DRG!
26 Nov 2019, RW Cox, @afni_refacer_run, level 3 (MAJOR), type 6 (ENHANCE) Modify shell dataset to avoid some brain clipping Mostly by eroding the inside of the brain shell. Also a couple little tweaks to the script.
23 Oct 2019, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 1 (NEW_PROG) Script to check properties of a dset, see if suitable for FS's recon-all. The check criteria have been built over time, empirically.
02 Oct 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL) The naming convention of PE dist dir has been reversed; mask opts changed. PE dist dir should match with JSONs better; 3dmask_tool does masking now.
12 Sep 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL) Output QC directory of images now, as well. Useful for quick QC. Later, will add some checks for obl, to not smooth unnec.

auto-generated by afni_history on Sep 1 2021