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) ---- 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.
29 Aug 2019, P Taylor, @auto_tlrc, level 3 (MAJOR), type 0 (GENERAL) RE-introducing the program '@auto_tlrc' to the distribution. It had been mistakenly deleted somehow.
23 Aug 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 4 (BUG_FIX) Fixed calculation when PE effective echo spacing is input. The conversion to BWPP was wrong; led to almost no distortion corr.
15 Aug 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL) This program has been pretty fully revamped, and might be worth using now. New scaling from Vinai, several updates/fixes/changes from last ver. 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, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Labels on stim regressors, vorig QC block added, grayplot pbvorder/enorm. Help updated; output stats still if not align/tlrc blocks used.
25 Jun 2019, P Taylor, 3dSkullStrip, level 3 (MAJOR), type 5 (MODIFY) Dset orient should no longer affect results (b/c of var of init cond). Intermediate resampling now reduces/removes var due to start.
22 May 2019, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Somewhat big changes: warns block updated and radcor block added. Left-right flip and @radial_correlate checks now in; other tweaks.
18 Apr 2019, P Taylor, @SSwarper, level 3 (MAJOR), type 2 (NEW_OPT) Include -deoblique and -giant_move opts. For oblique data, and/or heavily rotated, shifted, etc.
11 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV) Brainnetome atlas This atlas is now included in the standard distribution This also is in the default list of atlases
07 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV) Eickhoff-Zilles 2.2 MPM atlas This atlas is the newer 2.2 version of the MPM atlas This atlas replaced the 1.8 version in the list, but both are kept in the binary distribution
05 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV) HCP Glasser atlas in AFNI atlases Mike Beauchamp and Meghan Robinson contributed atlas Now included and first in default list too This atlas is in MNI space (not in its original Contee grayordinate surface space. Additionally, all the pmaps (probability maps) have been removed from the standard distribution and default list
07 Mar 2019, RC Reynolds, gen_ss_review_table.py, level 3 (MAJOR), type 2 (NEW_OPT) add -report_outliers and support options Add -report_outliers_{fill,header}_style, -write_outlier, and -outlier_sep for controlling the table presentation. Will use -write_table instead of -tablefile going forward.
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.
19 Dec 2018, P Taylor, @djunct_montage_coordinator, level 3 (MAJOR), type 4 (BUG_FIX) This montage coordinator was noooot picking the right vol to focus on. That should be fixed via magical incantations now.
23 Nov 2018, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Outputs JSON files now, for easier handling of information later. These provide more comprehensive info, as well as href linknames. 23 Nov 2018, P Taylor, apqc_make_html.py, level 3 (MAJOR), type 0 (GENERAL) Much better page formatting now, including navigation bar. User can jump to sections.
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.
20 Sep 2018, RW Cox, 3dttest++ etc., level 3 (MAJOR), type 6 (ENHANCE) ETAC now output global thresholds as well as local Global thresholds are text tables of cluster-size (or cluster-FOM) thresholds that apply to the whole volume in the multi-threshold way, rather than dataset tables that apply voxelwise. Moderately extensive hanges to programs 3dMultiThresh 3dXClustSim 3dttest++ and to support files mri_threshX.c thd_Xdataset.c 3dttest++ now has options to turn on/off global and local ETAC threshold calculations.
15 Aug 2018, RW Cox, 3dGrayplot, level 3 (MAJOR), type 6 (ENHANCE) Total rewrite of resampling from time+space to X+Y grid Grid refinement (time-X) is now cubic interpolation rather than linear Grid coarsening (space-Y) is now minimum sidelobe taper averaging rather than linear tapering
25 Jul 2018, P Taylor, @chauffeur_afni, level 3 (MAJOR), type 0 (GENERAL) Several new options, as well as ability to deal with 4D images. Many new features, probably including minor bug fixes.
24 Jul 2018, RC Reynolds, dcm2niix_afni, level 3 (MAJOR), type 6 (ENHANCE) version v1.0.20180622, including fix for enhanced DICOM Philips bvec/bval Update from C Rorden.
01 Jul 2018, P Taylor, @SSwarper, level 3 (MAJOR), type 2 (NEW_OPT) New opt: well, actually, it is new to *have* explicit options now! Same great functionality, but with more flexible options/names/outputs.
22 Jun 2018, RC Reynolds, dcm2niix_afni, level 3 (MAJOR), type 6 (ENHANCE) version v1.0.20180614, including JPEG-LS support Update from C Rorden.

auto-generated by afni_history on Jun 3 2020