AFNI HISTORY

level 2 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 2 -past_months 6 

---- 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.
02 Jun 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) Add PM (plus/minus) curve plotting options Added to the 'Colors Etc' menu. Curves, Bars, and Fill.
01 Jun 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) in populate_nifti_image(), call time series only if ntt>1 or NVALS==1 This is to avoid confusion when a time series is used to master a non-time series dataset. 01 Jun 2020, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_regs and -show_regs_style Show column indices or labels of an xmat.1D file with empty (all-zero) regressors. An index list can be space or comma-separeated, or encoded. Example 30 shows typical use cases. Added for S Haller. 01 Jun 2020, P Taylor, lib_mat2d_base.py, level 2 (MINOR), type 0 (GENERAL) Migrated from lib_mat2d.py; tweaks added. Add in few more mat2d attributes; rearrange methods. 01 Jun 2020, P Taylor, lib_mat2d.py, level 2 (MINOR), type 0 (GENERAL) Start some new functionality for 2D matrices. In particular, these are for 3dTrackID and 3dNetCorr output. 01 Jun 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) For vstat with seedbased corr (rest), use 0.2 as thr value of corr map. The value 0.3 seemed pretty high (esp. if no smoothing is applied). 01 Jun 2020, P Taylor, afni_base.py, level 2 (MINOR), type 0 (GENERAL) Add new funcs for convenient message printing, in the AFNI style. IP(), EP() and WP(), which are wrappers to use APRINT(). 01 Jun 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Reformat report*.1D tables a bit. Add in a KEY; change U/W to A/B; minor format stuff.
31 May 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Change range of grayscale when EPI is ulay (ve2a and LR flipcheck). Now 2-98percent (nonzero). 31 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX) Two bug fixes: 1) where src_prefix is defined. 2) Make sure labels/atlases of ATL|SEG followers are passed along.
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. 30 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) String selector of lost ROIs now is only comma-separated list. Discovered couldn't have both comma- and '..'-separated list in selector. 30 May 2020, P Taylor, @djunct_modal_smoothing_with_rep, level 2 (MINOR), type 0 (GENERAL) Now use *.nii.gz files for all intermeds, not *.nii. Works better with @animal_warper this way. 30 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Apply input_abbrev earlier in processing. Homogenize naming, I think, if it is being selected.
28 May 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) Add curve smoothing plot to graph viewer Invoked from 'Colors Etc' menu, or by pressing the 's' key. [For GC] 28 May 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Now report DF information in vstat block. Needed to be able to interpret F-stat and t-stat values.
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. 26 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Now output an AFNI-style string selector of 'lost' ROI values. This might make it easier to see the diffs the volumes.
25 May 2020, RC Reynolds, Makefile.macos_10.12_local, level 2 (MINOR), type 6 (ENHANCE) add libexpat.1.dylib to EXTRA_INSTALL_FILES R was upgraded to 3.6 (on the 10.12 build machine), since that is the current G Chen version requirement, making R_io.so work for people with only 3.6. But libexpat was upgraded too, which afni depends on, meaning systems needed that new version of libexpat, or afni would not work. Instead, libexpat.1.dylib is now simply included with the binaries. Thanks to S Gotts and K Tran for reporting the problem.
22 May 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) Change this prog to do all work in a workdir that can be cleaned. Should not have any effect on the usage or outputs.
21 May 2020, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 2 (NEW_OPT) add options -NN1, -NN2 and -NN3 Also, fix tiny origin shift when large zero-padding is applied. 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. 21 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Require mode_smooth_size as input, and include it in table. Thanks to D Glen and A Messinger for helpful feedback+inputs. 21 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Report now reports mode_smooth_size. Thanks to D Glen and A Messinger for helpful feedback+inputs.
20 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) update THD_mask_erode_sym() akin to take NN param This matches the dglen update to THD_mask_dilate(). 20 May 2020, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 4 (BUG_FIX) fix history and memory loss
19 May 2020, DR Glen, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT) nzvolume - volume of nonzero voxels
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. 18 May 2020, P Taylor, afni_seeds_per_space.txt, level 2 (MINOR), type 0 (GENERAL) Updated APQC seed locations for stereoNMT space. More centralized now in GM and in specific ROIs; aud away from vessel.
14 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Large number of under-the-hood changes, for readability/clarity. Change echo->printf, spacing, clear comments, etc. No output changes.
11 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) update web links to help pages in uber*.py Update uber_align_test.py, uber_skel.py, uber_subj.py and uber_ttest.py. 11 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) updates for python3 Update xmat_tool.py, quick.alpha.vals.py, read_matlab_files.py, uber_align_test.py and uber_skel.py.
04 May 2020, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 6 (ENHANCE) make partual updates for python3 04 May 2020, RC Reynolds, suma-general, level 2 (MINOR), type 5 (MODIFY) remove tabs from a bunch of files 04 May 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX) fix download of test file Thanks to Gerome on MB for reporting the problem. 04 May 2020, P Taylor, @Install_IBT_DATASETS, level 2 (MINOR), type 1 (NEW_PROG) Installer for the Indian Brain Templates. Enjoy.
30 Apr 2020, JK Rajendra, afni, level 2 (MINOR), type 0 (GENERAL) Added YouTube button to afni GUI.
29 Apr 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 5 (MODIFY) for recur, def to pub/dist/bin/misc; terminate on failed test download 29 Apr 2020, RC Reynolds, @chauffeur_afni, level 2 (MINOR), type 6 (ENHANCE) add AFNI_DRIVE_OPTS_XVFB env var for adding opts to Xvfb This will probably be modified later, but it allows one to pass something like '-nolisten inet6' if IPv6 is not working. Thanks to W-L Tseng.
27 Apr 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Added a help example for integrating output into afni_proc.py. ... because otherwise *I* forget how to use the outputs.
24 Apr 2020, P Taylor, 3dLMEr, level 2 (MINOR), type 0 (GENERAL) Updating this R file for GC. So I don't really know what the changes do. ... though I reeeallly want to pretend the changes were mine, ALL MINE. 24 Apr 2020, P Taylor, 3dClusterize, level 2 (MINOR), type 0 (GENERAL) Sidedness of testing will no longer be checked for non-stat thr vols. It must be Daniel Glen's birthday today (two-sided, non-stat p<0.9999).
23 Apr 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Added new help example. Demonstrates useful colorbar-entry functionality. 23 Apr 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Use '-colorscale_idx_file ..' to control AFNI env var AFNI_COLORSCALE_xx. Provides a way for user-created cbar info to be input+used.
21 Apr 2020, JK Rajendra, afni, level 2 (MINOR), type 2 (NEW_OPT) Added -all_dsets to load all datasets togther.
14 Apr 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX) if dataset inputs had full paths, use them in proc script Thanks to W-L Tseng for pointing out the discrepancy.
10 Apr 2020, RW Cox, AFNI gui, level 2 (MINOR), type 2 (NEW_OPT) Add -norm option for normal font sizes
08 Apr 2020, RW Cox, 1dplot, level 2 (MINOR), type 6 (ENHANCE) Add '0' to the -dashed option -dashed codes are now 1 = solid 2 = longer dashes 3 = shorter dashes 0 = no line, use boxes Code 0 is new, to allow a graph with some data plotted with lines and some without.
07 Apr 2020, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT) add -see_also and -ver_man to help create a quick man page To create a man page (via help2man), consider: nifti_tool -see_also > nt.see_also.txt help2man --help-option=-help --version-option=-ver_man \ --include nt.see_also.txt --no-info nifti_tool \ | gzip > nifti_tool_manpage.1.gz after which one can install the file, or test via man ./nifti_tool_manpage.1.gz (see the uncompressed version for syntax).
31 Mar 2020, RC Reynolds, neuro_deconvolve.py, level 2 (MINOR), type 6 (ENHANCE) update for python3 31 Mar 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 4 (BUG_FIX) fix lib_system_check:self.os_dist for newer python
30 Mar 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) have module_test_lib.py (and so afni_proc.py) work on python 2.6 again Done for S Horovitz. 30 Mar 2020, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) rigid_equiv - rigid equivalent affine alignment 30 Mar 2020, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX) NIFTI view equivalent for epi2anat alignment fix
27 Mar 2020, DR Glen, @animal_warper center_shift, level 2 (MINOR), type 2 (NEW_OPT) Allow for center shifting or not
24 Mar 2020, RC Reynolds, python_module_test.py, level 2 (MINOR), type 5 (MODIFY) restore approximate previous behavior
23 Mar 2020, RC Reynolds, 3drefit, level 2 (MINOR), type 2 (NEW_OPT) add options -oblique_recenter and -oblique_recenter_raw Adjust the origin so the cardinalized 0,0,0 (e.g. seen in the afni GUI) is in the same brain location as it was originally (in the scanner?). So when viewing an oblique volume on top of a '3dWarp -deoblique' output, coordinate 0,0,0 will match between them.
20 Mar 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY) fix PY_DIR, update PY vars, add list_py_libs 20 Mar 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY) fix PY_DIR, update PY vars, add list_py_libs
19 Mar 2020, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX) fix use of module_test_lib.py with change to new afnipy dir
17 Mar 2020, RW Cox, afni GUI, level 2 (MINOR), type 2 (NEW_OPT) Modify font size options - hopefully easier now 1) Change meaning of 'plus' fonts to be bigger than before. 2) Change so that 'plus' twice on command line equals 'big'. 3) Add simpler options '-big' and '-plus' and '-minus'. Combined, these should make it easier to do font size changes.
12 Mar 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) point web help for program to sphinx tree Also, added -hweb/-h_web for python progs that use option_list.py. 12 Mar 2020, RC Reynolds, SUMA_test_DrawingAreaWidget, level 2 (MINOR), type 1 (NEW_PROG) test for a valid DrawingAreaWidgetClass pointer 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. 12 Mar 2020, P Taylor, 3dReHo, level 2 (MINOR), type 0 (GENERAL) Alter output format if ROI neighborhood values of ReHo are calc'ed. Make 2 col (ROI val; ReHo val). Output multiple text files, if nec, too.
11 Mar 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Swap ulay/olay in va2t (anat->ulay); clearer image, maybe. Make template (if used) ulay in most other QC blocks.
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.
05 Mar 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 5 (MODIFY) for now, use mris_convert/3dcopy for extra annot files So standard mesh version will not have a proper label table, but the values will be appropriate and more usable in suma. This is done to import the Schaefer/Yeo atlases onto standard meshes. Done with D Glen.
27 Feb 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) add -fsannot_ver; apply -extra_annot_labels output as -extra_fs_dsets 27 Feb 2020, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) New opt '-warpscale' added; is a new opt in 3dQwarp, can be tweaked here now. Control flexibility of warps. Right now testing different values.
26 Feb 2020, RW Cox, machdep, level 2 (MINOR), type 6 (ENHANCE) First step for allowing floating round randomization Code in machdep.c, enabled by environment variable AFNI_RANDOMIZE_ROUNDING, lets a program invoke macro RAND_ROUND to randomize the IEEE rounding mode. This requires compiling with the flag -DUSE_FENV to enable use of the C99 function fesetround() to set the rounding mode -- see machdep.h. So far, only 3dAllineate has any parts that use RAND_ROUND -- that is, if you set AFNI_RANDOMIZE_ROUNDING to YES and run 3dAllineate, the results will change from a 'normal' run. How much? That's the point of this update, to see how sensitive the output is to the accumulation of tiny changes. 26 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Crashing in cases of 'pythonic' APQC with no censoring. Have fixed now. 26 Feb 2020, DR Glen, @animal_warper ROIdset followers, modal smoothing, level 2 (MINOR), type 2 (NEW_OPT) Allow for ROIs to follow into template space and modal smoothing ROIs are transformed with nearest neighbor interpolation Both ROIs and segmentation followers from the template space are now modally smoothed within 3 voxel neighborhoods
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. 25 Feb 2020, P Taylor, check_dset_for_fs.py, level 2 (MINOR), type 4 (BUG_FIX) Minor bug fix, caught by RCR. Or was it first *added* by RCR???? ... Nope. It was added by me. Sigh.
24 Feb 2020, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) Add -warpscale option To scale the warp displacments down at each level, for experimentation.
22 Feb 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) Temporary files now have a random string in their prefix. Thus, can have multiple runs in same directory simultaneously sans problem e. 22 Feb 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Can control AGIF frame rate, using opt (-agif_delay) to control AFNI env var. Thanks to RCR for pointing out the env var.
21 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Crashing in cases of 'basic' APQC with no outlier-based censoring. Have fixed now.
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. 19 Feb 2020, RC Reynolds, afni_util.py, level 2 (MINOR), type 5 (MODIFY) no longer available as a main executable 19 Feb 2020, P Taylor, adjunct_select_str.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_select_str.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_make_script_and_rst.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_is_label.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_is_label.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_combine_str.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_combine_str.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_calc_mont_dims.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_calc_mont_dims.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, DoPerRoi.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @DoPerRoi.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) New QC image outputs added. One for skullstripping (orig space) and one for warping (ref space).
18 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) help examples now include some developed outside of afni_proc.py This includes some class demos, along with pamenc and NARPS. Include a line about whether each example is reasonably recommended. Done to appease the mighty P Taylor.
17 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Reorganized under the hood, deal with censoring in a better way. Easier to tweak/update changes now. 17 Feb 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL) Opt -censor_hline can now take a keyword NONE as an entry. Useful if looking at multiple inputs and only some have censor lines.
14 Feb 2020, RW Cox, afni GUI, level 2 (MINOR), type 4 (BUG_FIX) Get Atlas Colors working again Problem: 2 generations of overlay colorization changes. a) Overlay went from indexes to RGB b) Overlay went from indexes or RGB to RGBA The atlas overlaying function didn't allow for these very well, especially the latter. Obviously, this can't be my fault since I'm the boss - even though I wrote the offending code. Someone must have joggled my brain. 14 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -compare_opts_vs_opts One can compare two afni_proc.py commmands sequentially, that are not part of the stored examples list. Consider: afni_proc.py ... first option set ... \ -compare_opts_vs_opts \ ... second option set ... It is okay for 'second option set' to include the afni_proc.py command name, in case two scripts are concatenated. 14 Feb 2020, DR Glen, @animal_warper dset followers, level 2 (MINOR), type 2 (NEW_OPT) -dset_followers to apply same transformations as dset 14 Feb 2020, DR Glen, @Align_Centers shift xform, level 2 (MINOR), type 2 (NEW_OPT) Move center/origin by known amount from 1D file Large translations in nonlinear warp interpolation can use vast amounts or memory in the 3dNwarpApply implementation. By doing center alignment separately, we can remove the memory and computational costs. The new options are -shift_xform and -shift_xform_inv.
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. 12 Feb 2020, DR Glen, 3dCM Icent, Dcent, level 2 (MINOR), type 2 (NEW_OPT) alternative centers To force centers to lie within a region -Icent for internal center, -Dcent for distance center
07 Feb 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) reduce X11 program deps Possibly define LLIBS_X11 in top-level Makefile (as current LLIBS) and then remove X libs from LLIBS. M.INCLUDE will define LLIBS if not set. Move suma_help to IMOBJS. 07 Feb 2020, RC Reynolds, Makefile.linux_fedora_28_shared, level 2 (MINOR), type 6 (ENHANCE) build main non-X11, non-SUMA AFNI program without X deps Set LLIBS_X11 to current LLIBS, and give it to SUMA_LINK_LIB. Remove all X11 libs from LLIBS. Add -DREPLACE_XT to CEXTRA. Note: without REPLACE_XT, LLIBS could still just use Xt and X11. And made the same mods to Makefile.linux_xorg7_64.
05 Feb 2020, RW Cox, 3dGrayplot, level 2 (MINOR), type 2 (NEW_OPT) Add -LJorder option To order voxels by their Ljung-Box statistics. 05 Feb 2020, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT) list all global options via 'PROG.py -optlist_show_global_opts' Also, add -optlist_show_argv_array to display afni_proc.py options in python dictionary format. This could be done with any OptionList-based python program. 05 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add inital new library for processing example, lib_ap_examples.py
03 Feb 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) add -extra_annot_labels 03 Feb 2020, P Taylor, @djunct_anonymize, level 2 (MINOR), type 1 (NEW_PROG) Anonymize files, and maybe add a note. Can either edit input directly, or make a copy + edit that. 03 Feb 2020, P Taylor, @afni_refacer_run, level 2 (MINOR), type 2 (NEW_OPT) Can anonymize output dsets: -anonymize_output. Fairly self-explanatory opt.
02 Feb 2020, RW Cox, 3dPval, level 2 (MINOR), type 2 (NEW_OPT) Add -qval option to 3dPVAL [for GC]. Merry Groundhog Day!
29 Jan 2020, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX) Couldn't deal with volumes that had RGB type, which happens for DEC maps. Has been fixed now. 29 Jan 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 4 (BUG_FIX) The input opt '-xfile ..' was broken; now it is fixed. Fix class inits, as well, under the hood.
27 Jan 2020, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE) add basis=BASIS parameter when defining timing class Done for geenaianni on MB. 27 Jan 2020, RC Reynolds, @diff.tree, level 2 (MINOR), type 2 (NEW_OPT) add -show_list_comp, to do pairwise comparison of file names 27 Jan 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE) gzip SUMA/*.nii, except for SurfVol 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. 27 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Fixed bug in QC. Broke when there was one stim used (bad scalar -> list conv).
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.
23 Jan 2020, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE) add handling of magic version 4 (ROIs and mask==1 data) Done for J Gonzalez-Castillo.
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 22 Jan 2020, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE) add handling of magic version 3 (all data light)
21 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Increase thresholds and cbar range in vstat_seedcorr and regr_corr dsets. Clearer QC, methinks, based on several different group dsets.
17 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) New pieces of QC: corr brain image in regr block. Shows corr of mean residual with everything. Have a nice day.
15 Jan 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) corr_* dsets are now correlations with ROI averages They were previously average correlations with each ROI voxel. The new maps look similar, but are probably more natural and have nicer scales. Requested by P Taylor.
14 Jan 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Change text of animal_outs.txt. Add in a couple new dsets to be listed.
13 Jan 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) add some make lists ; see 'make list_lists' 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). 13 Jan 2020, P Taylor, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) New function to read in seed list text file. Returns list of seed objs for APQC. 13 Jan 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT) Couple new options. Can specify colorbar and center coords now.
31 Dec 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY) Do not require out_limit. Currently will still show in driver. Done for P Taylor.
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 Dec 2019, P Taylor, check_dset_for_fs.py, level 2 (MINOR), type 4 (BUG_FIX) Fix one of the test criteria (-is_mat_even). Thanks, S. Torrisi, for pointing this out.
25 Dec 2019, DR Glen, erosion/dilation neighborhoods, level 2 (MINOR), type 5 (MODIFY) Allow for NN1,NN2,NN3 neighborhoods for erosion and dilation 3dAutomask and other programs use these functions the depth option in 3dAutomask gives a depth of automask NN1,2,3
17 Dec 2019, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE) allow labels as column selectors when reading xmat.1D files Done for G Chen.
12 Dec 2019, RW Cox, 3dTcorrelate, level 2 (MINOR), type 2 (NEW_OPT) Add -zcensor option Remove from consideration any time point t where xset(t) OR yset(t) is identically zero (in the mask). For Peter Molfese and Emily Finn. Merry X! 12 Dec 2019, DR Glen, @measure_erosion_thick, level 2 (MINOR), type 5 (MODIFY) More centers - find deepest near voxel closest to Center of Mass Came from CodeConvergence idea by Meghan Robinson Voxel closest to center of mass is similar to latest ICent in Clusterize GUI
10 Dec 2019, RW Cox, AFNI GUI, level 2 (MINOR), type 3 (NEW_ENV) Add 'Zoom lock' to the locking capability Also a new environment variable AFNI_ZOOM_LOCK to turn this on at startup, vs interactively later. 10 Dec 2019, RC Reynolds, uber_proc.py, level 2 (MINOR), type 5 (MODIFY) separate into main/lib/gui, so one can run -help w/out PyQt4
09 Dec 2019, RC Reynolds, 3dTagalign, level 2 (MINOR), type 2 (NEW_OPT) add -tagset Coded by T Holroyd.

auto-generated by afni_history on Jun 3 2020