AFNI HISTORY
level 1 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 1 -past_years 2
---- log of AFNI updates (most recent first) ----
09 Mar 2017, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
from D Warren: put exception handling around os.chmod calls
07 Mar 2017, RC Reynolds, RetroTS.py, level 2 (MINOR), type 4 (BUG_FIX)
from J Zosky: default to using numpy.flipud()
The flipud() function did not work in the original Matlab version,
but it does in numpy. Use the new -legacy_transform opt for old
(and presumably incorrect) results.
06 Mar 2017, RC Reynolds, RetroTS.py, level 1 (MICRO), type 5 (MODIFY)
change -p and -v args to be read as floats; apply min(p/n_trace)
06 Mar 2017, RC Reynolds, AFNI.afnirc, level 1 (MICRO), type 4 (BUG_FIX)
AFNI_COMPRESSOR can be set to GZIP, not gzip
03 Mar 2017, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
add optimally combined 'Opt Comb' merge method
Done with V Roopchansingh.
01 Mar 2017, RW Cox, 3dUnifize, level 3 (MAJOR), type 2 (NEW_OPT)
Add -EPI option, to unifize time series datasets.
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.
28 Feb 2017, RW Cox, 3dEmpty, level 1 (MICRO), type 2 (NEW_OPT)
Add -geom option = define dataset by a 'MATRIX(...)' string
27 Feb 2017, RW Cox, afni GUI, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_IMAGE_LABEL_IJK
If this variable is set to YES, then the image label overlay (chosen
from the intensity bar popup menu) will show the slice index instead of
the slice coordinate. (for PT)
24 Feb 2017, RW Cox, afni GUI, level 1 (MICRO), type 0 (GENERAL)
Turn off crosshairs and left-is-left if all inputs are image files.
Also, hide the help for 'afni -im' since AFNI can now read images
directly as 'datasets'.
22 Feb 2017, RW Cox, AFNI gui, level 1 (MICRO), type 5 (MODIFY)
Add VG painting effect to AFNI image viewer
Just for fun, please!
20 Feb 2017, RW Cox, 3dDespike, level 2 (MINOR), type 4 (BUG_FIX)
Scale factor bug
The program ignored the scale factors attached to short datasets.
If they were all the same, that was not a problem.
But if they differed, then that was a big problem.
That was fixed. Also, the output now is always in float format.
13 Feb 2017, RW Cox, 3dSharpen, level 1 (MICRO), type 1 (NEW_PROG)
Sharpening filter in 3D
09 Feb 2017, RW Cox, thresholding, level 2 (MINOR), type 3 (NEW_ENV)
Fix inconsistency in thresholding with short-valued bricks
In the AFNI GUI, thresholding is done with floats.
But in 3dmerge and in Clusterize, if the thresh brick is a short,
thresholding was done with shorts. And the user-supplied threshold was
ROUNDED -- so that a threshold of 2.2 would become 2, which means that a
value of 2 was OK -- which it shouldn't be. Solution: change those
places to threshold with floats. However, if someone wants to keep the
old way for compatibility, then they can set AFNI_OLD_SHORT_THRESH to
YES.
09 Feb 2017, P Taylor, @GradFlipTest, level 1 (MICRO), type 4 (BUG_FIX)
Some IF conditions gave problems; some option names were inconvenient.
They are now ex-parrots.
06 Feb 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 5 (MODIFY)
Should deal with subbrick selection now.
Works for ulay and olay sets in usual AFNI way.
03 Feb 2017, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
decay timing class now follows better distribution; new decay_old class
02 Feb 2017, RC Reynolds, steps_mac.rst, level 2 (MINOR), type 5 (MODIFY)
rewrite OS X install instructions to use 10.7_local and fink
02 Feb 2017, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY)
default mac package is now macosx_10.7_local
01 Feb 2017, RC Reynolds, afni_system_check, level 2 (MINOR), type 6 (ENHANCE)
updates for fink and homebrew
31 Jan 2017, RW Cox, minimize_in_1D func, level 1 (MICRO), type 0 (GENERAL)
Modify to be more robust (I hope).
Used in solving for inverse to mixed model ACF (e.g., to get FWHM).
31 Jan 2017, P Taylor, @SUMA_renumber_FS, level 2 (MINOR), type 5 (MODIFY)
Update region list to work with new FS 6.0 that came out a week ago.
Regions #3 and #42 (in FS file output) appear now; ~'leftover' GM.
30 Jan 2017, RW Cox, ccalc etc, level 1 (MICRO), type 6 (ENHANCE)
Add acfwxm function to parser programs
To compute the Full Width at X Maximum for the mixed ACF model, for
input parameters a,b,c at level x (0 < x < 1) = acfwxm(a,b,c,x)
27 Jan 2017, RC Reynolds, CA_EZ_atlas.csh, level 1 (MICRO), type 5 (MODIFY)
with -help, do not dump TT_N27 in current directory
Have script fail if any arguments are given (e.g. -help).
Fix in all bin dirs and under atlases.
27 Jan 2017, P Taylor, @GradFlipTest, level 3 (MAJOR), type 5 (MODIFY)
Totally revamped-- have real options, better funcs, output text file.
Meshes with other changes in 1dDW_Grad* and 3dDWItoDT.
27 Jan 2017, P Taylor, 3dDWItoDT, level 1 (MICRO), type 2 (NEW_OPT)
Miniscule new option, '-bmatrix_FULL' to have clearer usage.
Just copies functionality of cryptic '-bmatrix_Z'.
26 Jan 2017, RC Reynolds, Makefile.macosx_10.7_local, level 2 (MINOR), type 2 (NEW_OPT)
this is a new Makefile to prep for exec directory dynamic linking
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++.
25 Jan 2017, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
in 10.11+, check for DYLD variables via sub-shells
24 Jan 2017, RC Reynolds, align_epi_anat.py, level 1 (MICRO), type 6 (ENHANCE)
trap failure from main 3dAllineate call
23 Jan 2017, RW Cox, 3dAllineate, level 1 (MICRO), type 5 (MODIFY)
for ls, lpc, lpa: use -autoweight by default unless user changes it
The default weighting scheme was -autobox for all schemes. For ls, lpc,
lpa, the default is not -autoweight -- if the user changes the weight,
this won't be enforced.
23 Jan 2017, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 4 (BUG_FIX)
allow automatic use of the INSTANT timing class
20 Jan 2017, RC Reynolds, make_random_timing.py, level 3 (MAJOR), type 6 (ENHANCE)
advanced usage, program version 2.00
Essentially a new program. The user may now define timing classes for
stimulus and rest event types.
see: make_random_timing.py -help_advanced
Motivated by K Kircanski and A Stringaris.
19 Jan 2017, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
Give warning when -lpa or -lpc is used without -autoweight
At beginning and at end. Thanks to PT.
19 Jan 2017, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 6 (ENHANCE)
advanced version 2 mostly ready
Have -max_consec and -ordered_stimuli implemented in new version.
19 Jan 2017, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
fix for -final_anat
Thanks to N Anderson for noting the problem.
18 Jan 2017, RW Cox, 3dmerge, level 1 (MICRO), type 2 (NEW_OPT)
option -nozero will prevent output of an all zero dataset
18 Jan 2017, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 5 (MODIFY)
change example 3 to be with EPI masks
12 Jan 2017, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY)
First view of OLay: set sub-bricks to reasonable values
Where 'reasonable' is in the eye of RWCox.
12 Jan 2017, RW Cox, @snapshot_volreg, level 1 (MICRO), type 5 (MODIFY)
Crop the volume before snapshot-ing
Cropping helps remove lots of blank space in the output.
Also, compute the slice spacing in the montages adaptively from
the dataset dimensions.
12 Jan 2017, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
for 10.11+, make flat warning and summary comment consistent
11 Jan 2017, RW Cox, @snapshot_volreg, level 1 (MICRO), type 5 (MODIFY)
@snapshot_volreg has been replaced by the former @snapshot_volreg3
Also, replaced the use of the 'pam' functions with similar 'pnm'
functions, to help in portability to demented Linux systems.
11 Jan 2017, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 2 (NEW_OPT)
added some help: -help_advanced, -help_todo
10 Jan 2017, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY)
Change x,y signs in 'Go to atlas location' menu for SPM coords
Per the request of Todd Braver
05 Jan 2017, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
NIFTI output and output directories not always handled correctly or completely
03 Jan 2017, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 6 (ENHANCE)
merged mrt branch into master - prep for advanced timing
30 Dec 2016, RW Cox, 3dttest++, level 1 (MICRO), type 2 (NEW_OPT)
Add -ACF option -- to compute ACF parameters from residuals
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.
30 Dec 2016, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 5 (MODIFY)
Output new data sets of renumb'd values, more consistent than 'rank' ones.
Also output more tissue segmentation maps based on ROIs.
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
29 Dec 2016, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
remove case 16 (brainstem) from aparc+aseg.nii WM extraction in help
Thanks to P Taylor for noting this.
26 Dec 2016, P Taylor, thd_center, level 2 (MINOR), type 2 (NEW_OPT)
Extra argument in THD_cmass() and THD_roi_cmass().
Allows for local ijk coordinate output; updated other calling functions.
23 Dec 2016, P Taylor, 3dCM, level 2 (MINOR), type 2 (NEW_OPT)
Allow ijk coordinate output.
Will be in local orientation. Makes undumping after easier.
21 Dec 2016, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
Add '-wmask' option
Like '-wball', enhances the auto-generated weight in a region, but this
region is selected by a mask dataset.
21 Dec 2016, RW Cox, 3dQwarp, level 1 (MICRO), type 0 (GENERAL)
Add -awarp option, to save Allineate-to-Nonlinear warp only
If -allineate is used, the output WARP dataset is the catenated affine
transform from 3dAllineate and the nonlinear warp from Warpomatic. If
the user wants to keep the 'pure' nonlinear warp from Warpomatic, then
'-awarp' will do so, with a dataset containing the AWARP moniker.
20 Dec 2016, RW Cox, AFNI GUI, level 1 (MICRO), type 6 (ENHANCE)
Allow blowups for saved montage images
For @snapshot_volreg3 script, but of course anyone can use it now.
20 Dec 2016, RW Cox, 3dUnifize, level 1 (MICRO), type 5 (MODIFY)
Tweak to make sure tiny values aren't amplified much by -GM
Tiny positive values way outside the brain could get super-amplified by
the -GM switch, producing a 3D halo. This fix clips those off.
20 Dec 2016, P Taylor, fat_mvm_prep.py, level 1 (MICRO), type 2 (NEW_OPT)
New --unionize_rois option: affects GRID element selection.
Now can select union of matrix elements across group for MVM_tbl.
15 Dec 2016, RC Reynolds, column_cat, level 1 (MICRO), type 6 (ENHANCE)
allow for reading from stdin via either '-' or 'stdin'
09 Dec 2016, RC Reynolds, 3dTsplit4D, level 1 (MICRO), type 6 (ENHANCE)
allow for direct writing to NIFTI via prefix, e.g. result.nii
08 Dec 2016, RC Reynolds, 3dTsplit4D, level 2 (MINOR), type 2 (NEW_OPT)
add -digits and -keep_datum; other minor updates
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.
08 Dec 2016, RC Reynolds, plug_vol2surf, level 1 (MICRO), type 6 (ENHANCE)
add -cmask option to correspond with any auto non-zero mask
07 Dec 2016, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
check for python2 and python3
05 Dec 2016, RC Reynolds, timing_tool.py, level 1 (MICRO), type 5 (MODIFY)
allow *:1 (or *ANYTHING) to mean no event
This is in case someone also marries empty run events.
Done for R Kampe.
30 Nov 2016, RC Reynolds, afni-general, level 3 (MAJOR), type 6 (ENHANCE)
<> range selector can now take a comma-delimited list of integers
So for a dataset with interger values from 0 to 8, these commands
should produce identical resutls:
3dcalc -a DSET+tlrc -expr 'a*amongst(a,3,4,5)' -prefix JELLO
3dbucket 'DSET+tlrc<4,3,5>' -prefix JELLO
3dbucket 'DSET+tlrc<3..5>' -prefix JELLO
3dbucket 'DSET+tlrc<2.3..5.86>' -prefix JELLO
Of course, this will probably get further enhanced to a list of
float ranges. We shall see.
Comma-delimited labels should work now, with a plan to add general
labels that might define all GM or similar in a FreeSurfer dataset, say.
23 Nov 2016, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX)
Used to be able to have nans in sBL b/c of sqrt(neg-from-rounding).
Now IF condition to prevent that. Happy Thanksgiving.
23 Nov 2016, P Taylor, 3dNetCorr, level 2 (MINOR), type 4 (BUG_FIX)
Z-score WB maps were all zeros-> now have values.
Hopefully even the correct Z-values.
18 Nov 2016, RW Cox, afni GUI, level 1 (MICRO), type 6 (ENHANCE)
Add 'QUITT' command to the driver
Exits AFNI immediately, rather than calling the usual leisurely rundown.
For use in scripts, to save a little time.
18 Nov 2016, RC Reynolds, @Align_Centers, level 1 (MICRO), type 2 (NEW_OPT)
add -prefix option, to name output
17 Nov 2016, RW Cox, afni GUI, level 1 (MICRO), type 6 (ENHANCE)
Four new colorscales
17 Nov 2016, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
add some checks for flat_namespace on OS X
17 Nov 2016, DR Glen, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Ask suma to send current surface name to SUMA_OUTPLUG file or stdout
16 Nov 2016, P Taylor, 3dDWUncert, level 2 (MINOR), type 0 (GENERAL)
Check for singular values, so don't get crashes from GSL calcs.
These pretty much occur outside mask, but can also be inside mask.
16 Nov 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 0 (GENERAL)
Output b-values are now floats, not ints.
Seems necessary, depending on what user has input.
16 Nov 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 4 (BUG_FIX)
The -out_bval_col_sep used did nothing (after last changes).
Have returned it to functionality.
09 Nov 2016, RC Reynolds, to3d, level 1 (MICRO), type 5 (MODIFY)
and Dimon/Dimon1: siemens timing outside range is only a warning
09 Nov 2016, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT)
add -gert_chan_prefix
Done for W Luh.
08 Nov 2016, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
possibly invert slice order, as DICOM sorting might affect MRILIB_orients
Thanks to W Luh for noting the problem.
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).
04 Nov 2016, RW Cox, afni InstaCorr, level 2 (MINOR), type 6 (ENHANCE)
Two small changes
(1) Extend the range of the bandpass to allow up to 10Hz (formerly only
up to 1Hz). 10Hz = Nyquist frequency for TR=0.05s, which is pretty fast
for MRI -- but doable for single slice imaging.
(2) Add a #PC option, to compute principal components to use as global
orts.
03 Nov 2016, RW Cox, afni GUI, level 1 (MICRO), type 6 (ENHANCE)
Experiment with logging duration of use (only for me for now)
03 Nov 2016, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
Single slice dataset InstaCorr failed
Due to the 'roundtrip' index calculation giving a value outside the
dataset. This is now prevented.
02 Nov 2016, RW Cox, 3dTproject, level 1 (MICRO), type 5 (MODIFY)
Add warning message if DOF is less than 20
02 Nov 2016, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
handle 10.12 version string
01 Nov 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add PPI preparation options
Add -regress_skip_censor to omit 3dD -censor option.
Add -write_ppi_3dD_scripts with corressponding options
-regress_ppi_stim_files and -regress_ppi_stim_labels.
These make PPI pre and post regression scripts, along with
the main analysis script.
Done for S Haller.
24 Oct 2016, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
bandpass notes and reference; stronger warning on missing -tlrc_dset
Thanks to P Taylor.
20 Oct 2016, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY)
Don't get 'vedit' volume for threshold slice when OLay==Thr brick
When Clusterize is on, the steps are
1) create a new overlay volume that is 'edited' -- set to zero where Thr
is too small or cluster was too small -- this is on the OLay grid
2) colorization fetches 2D slices from OLay and Thr sub-bricks for
viewing, interpolated to the ULay grid, then processes them for display
(threshold+coloring)
But when OLay==Thr, and anything but NN interpolation is used at step 2,
then the visible shape of the clusters can change due to the
interpolation of the Thr slice after its volume was edited. To avoid
this, volume editing is now skipped when extracting the threshold slice
in step 2.
This artifact occurs because of the 'warp-on-demand' feature in AFNI,
which allows the display of overlays whose grid does not match the
underlay grid, combined with the nonlinear operations of thresholding
and clusterizing. Since DRG brought this to my attention, he has to
bring the cookies to the next group meeting.
20 Oct 2016, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
check -mask_import for reasonable voxel dimensions
13 Oct 2016, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fix -BminusA bug
double sign reversal == no sign reversal == not good for anyone
12 Oct 2016, RC Reynolds, RetroTS.py, level 1 (MICRO), type 5 (MODIFY)
updated Makefile.INCLUDE to distribute this
12 Oct 2016, P Taylor, 3dDWUncert, level 2 (MINOR), type 0 (GENERAL)
Now output progress; also, only divvy up non-zeros to proc.
Should be faster/better parallelized, also tell user about itself.
12 Oct 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 0 (GENERAL)
Now, automatically output RD if '-eigs' opt is used.
And the users of 3dTrackID say, 'Yaaaay'. Or 'Wha'evah!'.
11 Oct 2016, RC Reynolds, RetroTS.py, level 1 (MICRO), type 5 (MODIFY)
make top-level executable, remove 'style' lib, quotes, use lib_RetroTS
11 Oct 2016, P Taylor, 3dDWUncert, level 3 (MAJOR), type 0 (GENERAL)
Totally reprogrammed, mainly to use OpenMP and be fstr.
Also should be more generalized if b0 != 0.
11 Oct 2016, P Taylor, map_TrackID, level 1 (MICRO), type 0 (GENERAL)
Put integer variables in to not get lame warnings when building.
Things like 'pppp = fscan();', etc... Purely aesthetic changes.
09 Oct 2016, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
new options -mask_import, -mask_intersect and -mask_union
For J Stoddard and J Jarcho.
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.
30 Sep 2016, RW Cox, AFNI plugins, level 3 (MAJOR), type 0 (GENERAL)
A long list of little-used plugins has been disabled.
They can all be re-enabled by setting environment variable
AFNI_ALLOW_ALL_PLUGINS to YES.
Or each one can be individually re-enabled by setting environment
variable AFNI_ALLOW_somename_PLUGIN to YES, where the list of such
plugins can be found in file README.environment.
30 Sep 2016, RW Cox, AFNI GUI, level 1 (MICRO), type 6 (ENHANCE)
Let user specify length of adaptive mean Tran 1D function
Through environment variable AFNI_AdptMeanWidth
29 Sep 2016, RW Cox, 3dDespike, level 2 (MINOR), type 2 (NEW_OPT)
-NEW25 is a slightly more agressive approach
(a) uses 25 point running median instead of 9 for pre-filtering
(b) sets cut2=3.2 (4 MADs) instead of 4.0 (5 MADs)
29 Sep 2016, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY)
New 1D transform = AdptMean19 = 19 point adaptive local mean
28 Sep 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -regress_ROI[_PC]_per_run options, to make per-run regressors
Also, used 3dTproject to detrend PC regressors for appropriate censoring.
23 Sep 2016, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -select_runs option
19 Sep 2016, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
add glob2stdout, for converting glob forms to lists in stdout
19 Sep 2016, RC Reynolds, @move.to.series.dirs, level 1 (MICRO), type 2 (NEW_OPT)
add -glob, for processing glob forms via afni_util.py and xargs
16 Sep 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -radial_correlate option, to run @radial_correlate in proc script
16 Sep 2016, RC Reynolds, realtime_receiver.py, level 1 (MICRO), type 5 (MODIFY)
continue even if requested GUI fails
14 Sep 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
Have a new '-bmax_ref ...' option: if bref has b>0.
Won't have much effective change *yet*, but will later. Possibly.
13 Sep 2016, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT)
add -blip_opts_qw to pass options to 3dQwarp in the blip block
13 Sep 2016, RC Reynolds, 3dANOVA3, level 1 (MICRO), type 5 (MODIFY)
change 'illegal argument after' errors to something more specific
13 Sep 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 2 (NEW_OPT)
New opt -bref_mean_top to average over mean bref when b>0.
Also, totally reprogrammed most of interior; had been too scraggly.
31 Aug 2016, P Taylor, 3dSpaceTimeCorr, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed bug in yet-unreleased function... and also changed a feature.
Bug: ts = all0 -> GSL badness on some comp; now, exclude seedvox in corr.
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.
29 Aug 2016, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
add a few more DYLD_FALLBACK_LIBRARY_PATH tests
25 Aug 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix output.proc prefix in case -script has a path
Also, allow -mask_apply group in the case of -tlrc_NL_warped_dsets.
Thanks to C Capistrano and P Kim for noting the output.proc problem.
Thanks to C Connolly for noting the mask problem.
25 Aug 2016, RC Reynolds, afni_util.py, level 1 (MICRO), type 6 (ENHANCE)
add append flag to change_path_basename()
23 Aug 2016, RC Reynolds, file_tool, level 2 (MINOR), type 2 (NEW_OPT)
add -fix_rich_quotes; if fixing a script, convert rich quotes to ASCII
Done for G Chen.
22 Aug 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
save all '3dAllineate -allcostX' anat/EPI costs to out.allcostX.txt
This is another quailty control measure.
19 Aug 2016, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 6 (ENHANCE)
can use surf_mask to restrict surface clustering
Use '-uvar surf_mask' to restrict on_surface clustering to mask.
Append SSCS command to end of script and handle NIFTI surf_vol.
The surf_mask mas added for C Thomas.
19 Aug 2016, DR Glen, 3dLocalstat, level 2 (MINOR), type 4 (BUG_FIX)
Neighborhoods miscalculated
18 Aug 2016, P Taylor, 3dReHo, level 2 (MINOR), type 4 (BUG_FIX)
Used to not allow subbrik selection on input.
Now it does. Thanks to Daniel H. for pointing it out.
17 Aug 2016, DR Glen, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
History not updated properly on output with NIFTI dset1/anat
16 Aug 2016, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
look for new ACF/FWHM blur estimates
15 Aug 2016, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 6 (ENHANCE)
default clustsim method is now ACF
This marks afni_proc.py version 5.00.
o run 3dFWHMx with -ACF
o ACF and ClustSim files go into sub-directories, files_ACF/ClustSim
o -regress_run_clustsim now prefers arguments, ACF, FWHM, both, no
o default clustsim method is now ACF (via -regress_run_clustsim yes)
10 Aug 2016, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
in Makefile.INCLUDE, have afni depend first on libmri.a
09 Aug 2016, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY)
If A controller pops up with a negative x or y, move it
This is an attempt to overcome some peculiar bug in XQuartz on El
Capitan, where the A controller pops up, then disappears to a negative x
location (off screen).
09 Aug 2016, RW Cox, 3dAllineate, level 1 (MICRO), type 6 (ENHANCE)
Allow IDENTITY to specify the identity matrix for transformations
In options -1Dparam_apply and -1Dmatrix_apply -- to make resampling
simpler for the hopeless users out there
09 Aug 2016, DR Glen, @SUMA_MakeSpecFS, level 2 (MINOR), type 5 (MODIFY)
Atlasize original unranked datasets too. They will have more reliable indices than the ranked
06 Aug 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
mri_read_ascii: check comment_buffer before strdup
05 Aug 2016, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -marry_AM
Added for J Wiggins.
05 Aug 2016, RC Reynolds, uber_subject.py, level 1 (MICRO), type 5 (MODIFY)
make -help_install more current
04 Aug 2016, RW Cox, afni GUI, level 1 (MICRO), type 0 (GENERAL)
Changes to keep controller height from expanding on Linux
Of course, being on a Mac, I can't actually test this change.
04 Aug 2016, RW Cox, 1dsum, level 1 (MICRO), type 6 (ENHANCE)
Save # header lines from mri_read_1D; echo back in 1dsum output
For use in combining 3dClustSim outputs, for example.
01 Aug 2016, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
do more hunting and reporting on libgomp and libglib
01 Aug 2016, P Taylor, 3dRSFC, level 2 (MINOR), type 4 (BUG_FIX)
In cases of *very large* N_pts, an error message appeared-- no more.
Just changed default initialization of >f_N value.
25 Jul 2016, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
fixed attaching lone '-' to following label
No NI_malloc might lead to crash, and the '-' was overwritten.
23 Jul 2016, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
if empty regressor, check for -GOFORIT (only suggest if not found)
22 Jul 2016, RW Cox, 3dttest++, level 1 (MICRO), type 5 (MODIFY)
New -nocov option for used with -Clustsim
To avoid writing out the -covariates sub-bricks in the -Clustsim
operation. Not clear that it is useful otherwise.
21 Jul 2016, RW Cox, 3dttest++, level 1 (MICRO), type 5 (MODIFY)
if -clustsim, check for non-3D datasets (e.g., surfaces)
20 Jul 2016, RW Cox, 3dttest++, level 1 (MICRO), type 2 (NEW_OPT)
-tempdir for -Clustsim
14 Jul 2016, RW Cox, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
Fix problem with -resid combined with -clustsim
Program assumed prefix_resid was NIFTI format,so just add '.nii' if it doe
s have that already.
14 Jul 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
THD_open_tcat: print error and return NULL on bad wildcard match
11 Jul 2016, DR Glen, 3dWarp tta2mni grid dimensions bug, level 2 (MINOR), type 4 (BUG_FIX)
Ignored grid dimensions in transformation between Talairach to MNI
08 Jul 2016, RW Cox, 3dttest++, level 3 (MAJOR), type 6 (ENHANCE)
Extend -clustsim option
Covariates and centering
1- and 2-sided
unpooled and paired
1 sample as well as 2 sample
08 Jul 2016, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
add -read_all, in case it is useful for sorting (e.g. -order_as_zt)
Added for K Vishwanath.
07 Jul 2016, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
add -order_as_zt to re-order from -time:tz to -time:zt
07 Jul 2016, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
check for partial install of PyQt4 (might be common on OS X 10.11)
06 Jul 2016, RW Cox, 3dQwarp, level 1 (MICRO), type 6 (ENHANCE)
Allow .jpg or .png file as source/base 'dataset' for 2D warping
30 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow single volume EPI input (e.g. to test blip correction)
Also, auto -blip_forward_dset should come from tcat output.
30 Jun 2016, DR Glen, unWarpEPI.py anat to epi lpc+ZZ cost, level 2 (MINOR), type 4 (BUG_FIX)
Mistakenly used lpa for anat to epi alignment
29 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
can modify blip order; BLIP_BASE -> MEDIAN_BLIP; add BLIP_NOTE to help
29 Jun 2016, RC Reynolds, 3dfim, level 1 (MICRO), type 4 (BUG_FIX)
fix crash for dset open error with long dset name
Thanks to J Henry for reporting the problem.
29 Jun 2016, DR Glen, align_epi_anat.py flipping identity, level 2 (MINOR), type 4 (BUG_FIX)
Case of mistaken IDENTITY for check_flip option
27 Jun 2016, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
allow for blip datasets that are not time series
24 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -requires_afni_hist; warp vr_base to make final_epi dset
23 Jun 2016, RC Reynolds, plug_realtime, level 1 (MICRO), type 6 (ENHANCE)
show pop-up if user selects Mask Vals without 3D RT registrasion
Clarify this in the plugin Help. For L Li and V Roopchansingh.
23 Jun 2016, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 6 (ENHANCE)
allow to work with NIFTI template
22 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
do nothing, but work really hard at it
Rewrite EPI transformation steps by storing and applying an array
of transformations: this should make future changes easier.
22 Jun 2016, RC Reynolds, auto_warp.py, level 1 (MICRO), type 4 (BUG_FIX)
correctly check base.exists()
22 Jun 2016, RC Reynolds, @diff.tree, level 1 (MICRO), type 2 (NEW_OPT)
added -diff_opts; e.g. -diff_opts -w
22 Jun 2016, RC Reynolds, @diff.files, level 1 (MICRO), type 2 (NEW_OPT)
added -diff_opts; e.g. -diff_opts -w
21 Jun 2016, RW Cox, 3dmaskave, level 1 (MICRO), type 2 (NEW_OPT)
Add -perc option for percentile
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.
20 Jun 2016, P Taylor, 3dLombScargle, level 2 (MINOR), type 4 (BUG_FIX)
Fixing bug in delta F calculation.
What more needs to be said?
19 Jun 2016, DR Glen, align_epi_anat.py dset1/2 deobliquing, level 1 (MICRO), type 4 (BUG_FIX)
Using dset1/2 terminology forced deobliquing off
17 Jun 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
w/dglen, dsets with HEAD in prefix (but no suffix) could not be opened
16 Jun 2016, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 6 (ENHANCE)
EPI blip up/blip down distortion correction is ready
Thanks to S Torrisi and D Glen.
16 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if NLwarp but no EPI warp, no NL; fix refit of blip median datsets
User probably forgot -volreg_tlrc_warp, so warn them.
16 Jun 2016, P Taylor, 3dLombScargle, level 2 (MINOR), type 5 (MODIFY)
Changed how number of output points/freqs is calc'ed.
Should be more stable across group.).
14 Jun 2016, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT)
Option -FWHMdset allows specifying per-voxel blurring parameter
For use with 3dLocalACF and scripting. EXPERIMENTAL!
14 Jun 2016, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
Conversion to vector image fails for LARGE datasets
The final step in the conversion to vectim is scanning the data for
floating point errors (NaN, infinity). If there are more than 2^31-1
voxels, integer overflow caused problems. Fixed by making the loop
variables in the floatscan functions be size_t, not int. This problem
certainly lurks elsewhere in AFNI, waiting to pounce on Spaniards.
14 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -blip_forward_dset; if needed copy along any obliquity information
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.
14 Jun 2016, P Taylor, 3dLombScargle, level 2 (MINOR), type 5 (MODIFY)
Making this output 'one-sided' spectra now.
Easier for 3dAmpToRSFC calcs.
13 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -align_unifize_epi : 3dUnifize EPI before anat alignment
Thanks to D Glen and S Torrisi for suggesting it.
13 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add BLIP_BASE case for -volreg_align_to
Use warped median forward blip volume as volreg alignment base.
13 Jun 2016, P Taylor, 3dLombScargle, level 3 (MAJOR), type 5 (MODIFY)
Revamped LS program-- AGAIN**2!-- now has Welch windows+tapers.
Scaling properly/consistently, couple bug fixes.
13 Jun 2016, DR Glen, 3dTstat - single sub-bricks, level 2 (MINOR), type 2 (NEW_OPT)
For datasets with only a single sub-brick, 3dTstat would exit
with an error for many statistics. The new behavior makes the
program use the first value of the time series instead. Some other
requested statistics like the argmax type stats are now calculated
even for this trivial case. Optionally the user may use
-firstvalue for a statistic
10 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -blip_reverse_dset for blip up/blip down distortion correction
09 Jun 2016, RW Cox, 3dLocalACF, level 2 (MINOR), type 1 (NEW_PROG)
Estimate ACF parameters locally. Slow and experimental.
09 Jun 2016, P Taylor, 3dLombScargle, level 3 (MAJOR), type 5 (MODIFY)
Revamped LS program-- AGAIN-- now has Welch windows+tapers.
Several new options added (related to windows/tapers).
03 Jun 2016, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT)
-wtprefix to save computed weight to dataset
03 Jun 2016, DR Glen, 3dQwarp bug, level 2 (MINOR), type 4 (BUG_FIX)
bug fix in option processing
Fixed wtprefix handling and gridlist option handling (with RCR)
02 Jun 2016, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Creation of All_Datasets session
If more than one session is input or created, then the All_Datasets
session is created as the catenation of all of them. This will help
people who want to look at data in multiple directories without moving
them together.
02 Jun 2016, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
w/dglen: read num slices from Siemens 3D acquisition DICOM image files
01 Jun 2016, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 6 (ENHANCE)
minor updates to verbose output
27 May 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
Have a new '-scale_out_1000' option: rescale output, if desired.
Effectively: change output diff units of mm^2/s -> x10^{-3} mm^2/s.
24 May 2016, RW Cox, 3dUnifize, level 2 (MINOR), type 5 (MODIFY)
Alter default -clfrac value to 0.2
Because old 0.1 default would often have too much noise outside the head
when used with non-skull-stripped datasets. User can still set '-clfrac
0.1' if needed.
24 May 2016, RW Cox, 3dQwarp, level 1 (MICRO), type 5 (MODIFY)
Remove second cubic and quintic iterations at lev=0
Repeating these iterations almost never does any good, and takes up a
fair amount of time.
24 May 2016, P Taylor, 3dLombScargle, level 3 (MAJOR), type 5 (MODIFY)
Revamped LS program-- new implementation, directly from PR89.
Several new options added (normalize, amplitudeize, etc.).
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
20 May 2016, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY)
alter 'Jumpto OLay Max/Min @Thr' menu button backgrounds to black
Because I find them hard to find; from Hangzhou China - Ni Hao!
20 May 2016, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
add options -dot_file_list/_pack/_show
List, package (tgz) or show the contents of found 'dot' files.
19 May 2016, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
-wball = emphasize some (spherical) region in the weighting
Written in Hangzhou China -- for Peng
19 May 2016, RC Reynolds, dicom_hdr, level 1 (MICRO), type 4 (BUG_FIX)
do not crash on missing input
17 May 2016, RW Cox, 3dUnifize, level 1 (MICRO), type 4 (BUG_FIX)
-ssave option caused a crash :-(
fixed in Hangzhou China
17 May 2016, RW Cox, 3dTshift, level 1 (MICRO), type 5 (MODIFY)
Update error messages to be more informative
To find problem in unWarpEPI.py script - from Hangzhou China
16 May 2016, DR Glen, align_epi_anat.py - left/right test, level 2 (MINOR), type 2 (NEW_OPT)
left/right checking using align_epi_anat.py
flipped datasets go unnoticed even in major publicly available
databases (initially noted by Brad Buchsbaum with FCON1000).
Now automatically determine mismatch in L/R with simple test
New -check_flip and -flip_giant options check alignment against
flipped data.
15 May 2016, RW Cox, 3dNwarpApply, level 1 (MICRO), type 5 (MODIFY)
Update error messages yet again (a little)
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.
06 May 2016, RW Cox, afni GUI, level 1 (MICRO), type 2 (NEW_OPT)
-XXXnpane to set number of panes in pbar
For the elusive ZXu, man of many nations.
05 May 2016, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT)
Option -percentile P
Computes the Pth percentile 0 <= P <= 100 of the data in each voxel.
Can only be used once per run!
05 May 2016, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY)
-defaults similarly implies -do_dotfiles and apsearch yes
04 May 2016, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
-dsort always produced the _nods dataset; now, only if -nods is used
04 May 2016, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY)
add -do_dotfiles and -do_extras
Running apsearch and possibly editing dot files is only on request.
03 May 2016, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
suggest -regress_est_blur_epits for resting state
Thanks to S Torrisi for bringing up the question.
03 May 2016, P Taylor, @GradFlipTest, level 2 (MINOR), type 5 (MODIFY)
Using '-out_grad_cols_bwt' for grad stuff now-- use weights.
Can deal well with multiple DW factors in gradient list now.
03 May 2016, DR Glen, whereami - atlas queries, level 1 (MICRO), type 4 (BUG_FIX)
Removing structures that are all numbers was breaking atlas label queries
03 May 2016, DR Glen, @Atlasize no voxel regions, level 1 (MICRO), type 2 (NEW_OPT)
Skip structures with no voxels
New -skip_novoxels option in @Atlasize and @MakeLabelTable
02 May 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
Have a new '-min_bad_md' option: use to threshold badness.
Also now detect bad DT fits if MD is crazy big. Whoa.
28 Apr 2016, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT)
add -local_package, to use an already downloaded package
Requested by P Taylor.
28 Apr 2016, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
add initial #!prog to tops of some meica programs, and bricks_test.sh
This corresponds with -x permission clearing by yarikoptic.
28 Apr 2016, RC Reynolds, 3dMVM.R, level 1 (MICRO), type 5 (MODIFY)
prevent any unexpected writing of dbg.AFNI.args files
Only write such files given -dbg_args.
Affects 1dRplot, 3dLME, 3dMEMA, 3dMVM, 3dPFM, 3dRprogDemo
3dSignatures, AFNIio, ExamineXmat, rPkgsInstall.
The dbg files no longer start with '.'.
27 Apr 2016, RW Cox, afni + 3dGroupInCorr, level 1 (MICRO), type 0 (GENERAL)
Remind user of what to do after 3dGIC connects to afni GUI
This is the Caballero-Rossi popup reminder.
27 Apr 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
prep for later: always extract volreg base, as vr_base*
26 Apr 2016, RC Reynolds, tokens, level 1 (MICRO), type 6 (ENHANCE)
handle arbitrarily long tokens
26 Apr 2016, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
Makefile.INCLUDE: moved SCRIPTS into scripts_install
25 Apr 2016, DR Glen, afni GUI perc threshold flag, level 1 (MICRO), type 4 (BUG_FIX)
percentile thresholding didn't work properly with warp-on-demand between views
20 Apr 2016, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY)
new Jumpto IJK for Overlay button
For someone in the Tulsa class :)
19 Apr 2016, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
incorrectly reported 'IFM:RIF fatal error' for the case of no sorting
Thanks to I Groen for reporting the problem.
19 Apr 2016, DR Glen, unWarpEPI.py, level 2 (MINOR), type 1 (NEW_PROG)
blip-up/down distortion correction script
18 Apr 2016, RW Cox, afni GUI, level 1 (MICRO), type 3 (NEW_ENV)
Open all 3 image viewers by default
New variables AFNI_OPEN_AXIAL (etc.) will turn off axialimage viwer (etc.)
if set to NO -- for LIBR and Tulsa.
18 Apr 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
THD_open_tcat: fix wilcard input lacking sub-brick selectors
Forgot to regenerate catenated list, dlocal.
18 Apr 2016, RC Reynolds, 3dbucket, level 1 (MICRO), type 6 (ENHANCE)
if THD_open_one_dataset fails, fall back to THD_open_dataset
As with 3dTcat, fall back rather than failing outright.
15 Apr 2016, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
added help macro CATENATE_HELP_STRING
This displays a 'CATENATED AND WILDCARD DATASET NAMES' section in the
help output from afni and 3dcalc (following 'INPUT DATASET NAMES').
15 Apr 2016, RC Reynolds, NIFTI-2, level 1 (MICRO), type 5 (MODIFY)
print int64_t using PRId64 macro, which looks ugly, but avoids warnings
14 Apr 2016, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY)
Make AFNI_FLASH_VIEWSWITCH turn off all obnoxious stuff
For Mr Neon (or is that Dr Neon?)
08 Apr 2016, RW Cox, afni GUI, level 1 (MICRO), type 2 (NEW_OPT)
Add '-XXX defaults'
08 Apr 2016, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
auto-tcat inputs with spaces, wildcards and global selectors
For example, input of 'DA*.HEAD DB*.HEAD DC*.HEAD[3,4]' would create
a dataset with sub-bricks 3 and 4 from all D[ABC]*.HEAD datasets.
If sub-brick selectors appear only at the end, they are global,
otherwise they can be per input, as in 'DA*.HEAD[0,1] DB*.HEAD[2,3]'.
08 Apr 2016, P Taylor, 3dDTtoDWI, level 2 (MINOR), type 5 (MODIFY)
Work to deal with bvalue-weighted grads.
This is useful esp. for new TORTOISE outputs.
07 Apr 2016, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_GIC_DEBUG=YES will cause lots of debugging printouts
For Sharyn and Cesar.
07 Apr 2016, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT)
add options -proto and -test_proto
One can specify the download protocol as http, https or NONE.
07 Apr 2016, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY)
switch to have cjpeg depend on libjpeg.a, so it does not get rebuilt
05 Apr 2016, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
fix bug with -5final -- but still hide from user
05 Apr 2016, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
THD_open_tcat works as wildcard - can apply sub-brick selectors
05 Apr 2016, P Taylor, 3dDWUncert, level 2 (MINOR), type 2 (NEW_OPT)
New inp format option-- for dealing with TORT export/import.
-bmatrix_Z for reading in bmat in AFNI format; byebye -bmatr opt.
05 Apr 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 2 (NEW_OPT)
New I/O options-- for dealing with TORT export.
Now have I/O of grad columns weighted by bvalues.
04 Apr 2016, RC Reynolds, THD_load_tcat, level 2 (MINOR), type 4 (BUG_FIX)
set factors and labels at open time, not at load time
This fixes use with 3dcalc and 3dinfo, though stats are not yet loaded.
04 Apr 2016, RC Reynolds, 3dTcat, level 1 (MICRO), type 6 (ENHANCE)
if THD_open_one_dataset fails, fall back to THD_open_dataset
Fall back rather than failing outright.
31 Mar 2016, RC Reynolds, 3dMVM.R, level 1 (MICRO), type 5 (MODIFY)
do not create .dbg.AFNI.args files on -help usage
Modified 1dRplot.R, 3dLME.R, 3dMEMA.R, 3dMVM.R, 3dPFM.R, 3dRprogDemo.R,
3dSignatures.R, ExamineXmat.R and rPkgsInstall.R.
30 Mar 2016, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE)
possibly update .bashrc if .cshrc is updated
29 Mar 2016, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 5 (MODIFY)
3dMEMA no longer allows for a paied test
One must now input contrast/stat from original regression.
29 Mar 2016, RC Reynolds, afni_restproc.py, level 1 (MICRO), type 5 (MODIFY)
suggest that users consider afni_proc.py
This was requested by Rayus.
29 Mar 2016, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 2 (NEW_OPT)
add option -no_cert_verify, to skip server certificate verification
26 Mar 2016, RC Reynolds, to3d, level 1 (MICRO), type 4 (BUG_FIX)
another allowance for datasets exceeding 2 GB
Thanks to SS Kim for noting the problem.
25 Mar 2016, RW Cox, afni GUI, level 2 (MINOR), type 2 (NEW_OPT)
A bunch of '-XXX' options to control colors and fonts
24 Mar 2016, RW Cox, afni GUI, level 1 (MICRO), type 2 (NEW_OPT)
Add -XXX option
Moving towards letting user set X11 things (fonts, colors) on the
command line. Still needs work, but has some functionality now for the
true Jedi AFNI Master.
24 Mar 2016, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT)
add option -use_obl_origin, to apply -oblique_origin to to3d command
Also, run any to3d script via 'tcsh -x' so the users get to see.
22 Mar 2016, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
modularize version checking
Update .afni.vctime even if URL read fails, to not flood server.
21 Mar 2016, RC Reynolds, uber_subject.py, level 1 (MICRO), type 6 (ENHANCE)
run GLTsymtest on specified GLTs
21 Mar 2016, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
get slightly more accurate motion ave via 3dTstat -nzmean
21 Mar 2016, RC Reynolds, GLTsymtest, level 1 (MICRO), type 2 (NEW_OPT)
added -badonly, to avoid screen clutter from many good GLTs
21 Mar 2016, RC Reynolds, 3dANOVA, level 1 (MICRO), type 6 (ENHANCE)
allow for up to 666 observations
Consider changing this to use a string_list or something similar.
17 Mar 2016, RW Cox, 3dTproject, level 2 (MINOR), type 4 (BUG_FIX)
Fix problem in setting count of bandpass regressors
Typo meant that Nyquist frequency might not be counted properly,
resulting in bad stuff (memory corruption).
17 Mar 2016, RW Cox, dataset input, level 1 (MICRO), type 6 (ENHANCE)
Input random dataset or 1D file on command line
jRandomDataset:64,64,32,22 creates a random dataset with nx=64, ny=64,
nz=32, and 22 time points.
jRandom1D:128,16 creates a random 1D file with 128 rows and 16 columns.
These are shortcuts for testing programs, which avoid having to create
temporary files via 3dcalc (say). In other words, these 'inputs' are
testaments to my preference to write C code than do actual work.
15 Mar 2016, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
-help_basis update: max convolved BLOCK() is ~5.1, not ~5.4
10 Mar 2016, RW Cox, debugtrace.h, level 1 (MICRO), type 5 (MODIFY)
Output command line, if available, in crash report
08 Mar 2016, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY)
Turn Auto-scaling on in graph windows by default
08 Mar 2016, RW Cox, 3dvolreg, level 1 (MICRO), type 5 (MODIFY)
Default resampling now heptic, not Fourier.
08 Mar 2016, RW Cox, 3dTproject, level 1 (MICRO), type 5 (MODIFY)
Add STATUS calls to 3dTproject for debugging
07 Mar 2016, RW Cox, 3dDeconvolve, level 1 (MICRO), type 5 (MODIFY)
Double default size of Xmat JPEG file
To avoid losing resolution when looking at TENT designs.
07 Mar 2016, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed edge option change using too small neighborhood size
01 Mar 2016, RC Reynolds, tokens, level 2 (MINOR), type 1 (NEW_PROG)
program to extract valid text entries from a file
01 Mar 2016, RC Reynolds, GIFTI, level 1 (MICRO), type 4 (BUG_FIX)
applied R Vincent fix for GIFTI datasets with Windows-style newlines
29 Feb 2016, RC Reynolds, 3dANOVA3, level 1 (MICRO), type 6 (ENHANCE)
show prior options to any 'Unrecognized command line option'
Added disp_strings() to libmri.a.
24 Feb 2016, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
replace tlrc_no_ss with anat_has_skull toggle and move to anat block
24 Feb 2016, RC Reynolds, timing_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
fix -warn_tr_stats crash on empty timing file
Thanks to Z Reagh for noting the problem.
22 Feb 2016, RW Cox, debugtrace.c, level 1 (MICRO), type 2 (NEW_OPT)
Colorize WARNING and ERROR message prefixes.
Can turn off by setting AFNI_MESSAGE_COLORIZE to NO. For Javier.
19 Feb 2016, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
add many tests and summarize potential issues
17 Feb 2016, RC Reynolds, afni_util.py, level 1 (MICRO), type 6 (ENHANCE)
add function affine_to_params_6: where input is 12 element sub-matrix
16 Feb 2016, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE)
add -ver and initial version reporting
11 Feb 2016, RW Cox, 3dttest++, level 3 (MAJOR), type 2 (NEW_OPT)
-clustsim option
This option runs 3dttest++ with -randomize and then 3dClustSim with
-inset, to produce cluster-threshold tables for inclusion in the output.
It is my intention that this method will replace the use of 3dFWHMx and
3dClustSim. Knock wood, and help Make AFNI Great Again!
11 Feb 2016, RW Cox, afni version check, level 1 (MICRO), type 0 (GENERAL)
add https support to thd_http.c
Via wget or curl, plus popen+fread+pclose. Cheap, but works.
11 Feb 2016, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 2 (NEW_OPT)
Add -ztest option == test inputs if they are all zero
For Cesar.
10 Feb 2016, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
full update to use https://afni.nimh.nih.gov (no longer http)
10 Feb 2016, RC Reynolds, @ANATICOR, level 1 (MICRO), type 4 (BUG_FIX)
fixed -radius option parsing
Thanks to A Frithsen for noting the problem.
10 Feb 2016, DR Glen, afni, level 1 (MICRO), type 4 (BUG_FIX)
fixed ignoring of -no1D option, and 1D files are not read on input
09 Feb 2016, RW Cox, 3dQwarp, level 1 (MICRO), type 0 (GENERAL)
Tested on 2D images (single-slice datasets)
It actually worked. Added a comment to that effect in the help output.
09 Feb 2016, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 2 (NEW_OPT)
-read option
To 'read()' data in, instead of 'mmap()' -- for network mounted data
where 'mmap()' fails to work. For Cesar Caballero.
09 Feb 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
be sure isfinite is defined in FD2_inc.c, parser_int.c
09 Feb 2016, RC Reynolds, @GradFlipTest, level 1 (MICRO), type 5 (MODIFY)
trap for missing inputs (e.g. used with just -help)
08 Feb 2016, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY)
access afni site via https protocol
05 Feb 2016, RW Cox, 3dClustSim, level 3 (MAJOR), type 2 (NEW_OPT)
New -inset option
Directly give the simulations, rather than generate them internally.
Intended for use with '3dttest++ -randomsign N -toz' and '3dttest++
-resid' to get the cluster thresholds directly from the data rather than
assumptions of Gaussianity.
05 Feb 2016, RW Cox, 3dttest++, level 1 (MICRO), type 5 (MODIFY)
Add number of iterations to -randomsign option
For use with 3dClustSim -inset
05 Feb 2016, RC Reynolds, thd_niftiread, level 1 (MICRO), type 4 (BUG_FIX)
NIFTI files with no *form_codes should default to +orig, not NIFTI_default
28 Jan 2016, RC Reynolds, 3dMean, level 1 (MICRO), type 5 (MODIFY)
fix help to correctly report -stdev as sqrt(var) {was var/(n-1)}
Thanks to K Kerr (MB) for pointing out the mistake.
27 Jan 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow for tissue based regression with only regress block
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.
22 Jan 2016, RW Cox, 1deval, level 1 (MICRO), type 2 (NEW_OPT)
Fixed value assignments, as in '-a=3.7'
For my convenience
22 Jan 2016, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
rigid_body alignment option and better handling of user allineate options
22 Jan 2016, DR Glen, auto_warp.py, level 1 (MICRO), type 4 (BUG_FIX)
skip_affine option previously skipped
22 Jan 2016, DR Glen, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
Incorrect check for file output existence for oblique data
06 Jan 2016, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
new -pnm option, to save to PNM image format
To make it easier to manipulate results in scripts (e.g., pnmcat).
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.
04 Jan 2016, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
add boundardy checks in get_1dcat_intlist and get_count_intlist
Without the checks, using count or 1dcat as sub-brick selector method
would lead to confusing crashes (if values exceedded #vols).
Thanks to W Graves for reporting the problem.
04 Jan 2016, P Taylor, 1dDW_Grad_o_Mat, level 1 (MICRO), type 4 (BUG_FIX)
Fixed backwards output messages.
Should now be easier to see what went bad in a case of mistaken input.
03 Jan 2016, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
truncate 'top history' text for data trees
31 Dec 2015, RW Cox, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
Don't allow -resid and -zskip at the same time
Because sorting out the residuals back to their proper places would
be hard, if some inputs were skipped.
31 Dec 2015, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
include AFNI_version_base.txt in build of afni_src.tgz
30 Dec 2015, RW Cox, 3dBlurToFWHM, level 2 (MINOR), type 2 (NEW_OPT)
add -acf option, to estimate FWHM via the ACF method
30 Dec 2015, RC Reynolds, afni-general, level 3 (MAJOR), type 6 (ENHANCE)
w/DRG implement new version system
See https://afni.nimh.nih.gov/pub/dist/MOTD/MOTD_2015_12_30.txt .
29 Dec 2015, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 4 (BUG_FIX)
catch any empty directory listing from @FindAfniDsetPath
29 Dec 2015, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
updated gitignore.src.txt and main 2 .gitignore files
29 Dec 2015, RC Reynolds, @FindAfniDsetPath, level 1 (MICRO), type 5 (MODIFY)
0 or bad # args returns 1 rather than 0
28 Dec 2015, RC Reynolds, @diff.files, level 1 (MICRO), type 6 (ENHANCE)
allow diffs to include existence of directories
22 Dec 2015, RW Cox, 3dvolreg, level 1 (MICRO), type 5 (MODIFY)
Make '-final linear' work, and put it in the help output.
For Daniel Handwerker. Don't say I never gave you a Christmas present!
19 Dec 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
removed CSFe from Example 10 of the help, to not lead people to use it
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 Dec 2015, RW Cox, afni Clusterize, level 1 (MICRO), type 6 (ENHANCE)
Add 'large FDR q' warning to Clusterize report
09 Dec 2015, RW Cox, 3dFWHMx, level 1 (MICRO), type 6 (ENHANCE)
Add the 'classic' Gaussian ACF to the '-acf' plot, for comparison.
08 Dec 2015, RW Cox, afni Clusterize, level 2 (MINOR), type 5 (MODIFY)
Add Write button to save just one cluster to a dataset
08 Dec 2015, RW Cox, 3dttest++, level 1 (MICRO), type 5 (MODIFY)
Allow constant value with -singletonA instead of a dataset
Allows user to test -setB against a nonzero constant.
07 Dec 2015, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT)
Add -resid option, to save residuals.
07 Dec 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
help update: modify example 11 to use SurfVol and add FREESURFER NOTE
07 Dec 2015, RC Reynolds, MatAFNI_Demo.m, level 1 (MICRO), type 4 (BUG_FIX)
merge fix from J. Pfannmoller
Done with G Chen.
01 Dec 2015, RW Cox, 3dClustSim, level 3 (MAJOR), type 2 (NEW_OPT)
Added -acf option!
Non-Gaussian spherically symmetric AutoCorrelation Function (ACF) for
the noise. Uses FFTs to create the noise fields, via #include-d file
mri_radial_random_field.c and #include-d csfft_OMP.c (thread-safe FFTs).
This method in 3dFWHMx and 3dClustSim will be the favored cluster
thresholding analysis going forward.
30 Nov 2015, RW Cox, csfft_OMP, level 1 (MICRO), type 0 (GENERAL)
Thread-safe version of csfft function, for use with OpenMP
Meant to be #include-d into the main source file.
27 Nov 2015, RW Cox, 3dFHWMx, level 1 (MICRO), type 5 (MODIFY)
OpenMP-ize the FWHM and ACF calculations (across sub-bricks)
Also, working on spherical non-Gaussian convolution by FFTs in
mri_radial_random_field.c
23 Nov 2015, RW Cox, many, level 1 (MICRO), type 0 (GENERAL)
Tiny edits to eliminate compiler warnings from icc
For example, change format '%ld' to '%lld' for numerous int64_t
printouts in nifti/cifti codes. Change 'finite()' to 'isfinite()'.
17 Nov 2015, RC Reynolds, afni-general, level 1 (MICRO), type 0 (GENERAL)
rename g_info to g_dicom_ctrl to avoid FreeBSD build conflict
Thanks to J Bacon for noting the conflict.
16 Nov 2015, P Taylor, 3dTrackID, level 3 (MAJOR), type 0 (GENERAL)
Estimate mean and stdev of fiber lengths in bundles.
These are now automatically output in *.grid file.
16 Nov 2015, P Taylor, 3dTrackID, level 3 (MAJOR), type 2 (NEW_OPT)
Can limit tracts to 'between targets' in new ways.
See '-targ_surf_stop' and '-targ_surf_twixt' in the help.
16 Nov 2015, P Taylor, fat_mat_sel.py, level 2 (MINOR), type 5 (MODIFY)
New default for x-axis labels: rot=45 deg, horiz align=right.
Better than previous defaults (rot=37 deg, horiz align=center).
10 Nov 2015, RW Cox, 3dFWHMx, level 3 (MAJOR), type 2 (NEW_OPT)
-ACF option to compute spatial autocorrelation function
For enhancing 3dClustSim, et cetera.
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.
06 Nov 2015, RC Reynolds, to3d, level 1 (MICRO), type 6 (ENHANCE)
allow for single volumes beyond 2^31-1 bytes
Done for Z Saad.
06 Nov 2015, RC Reynolds, @Align_Centers, level 1 (MICRO), type 2 (NEW_OPT)
add option -cm_no_amask; like -cm but without -automask
04 Nov 2015, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
add -slice_order_to_times
This converts a list of slice indices (sorted by acq time)
to slice times (ordered by index).
30 Oct 2015, RW Cox, images_equal, level 1 (MICRO), type 1 (NEW_PROG)
Tests if 2 input 2D image files are equal.
28 Oct 2015, RW Cox, 3dQwarp, level 1 (MICRO), type 5 (MODIFY)
Allow minpatch to go as low as 5.
Of course, such a small patch will be VERY slow indeed. Also, bring out
of hiding the '-ballopt' option, which changes the optimization strategy
somewhat -- allowing for larger displacments in the incremental warps.
28 Oct 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
output anat/EPI Dice coefficient, rather than correlation
28 Oct 2015, RC Reynolds, 3ddot, level 2 (MINOR), type 2 (NEW_OPT)
add -dodice, to get the Dice coefficient
28 Oct 2015, RC Reynolds, gen_ss_review_table.py, level 1 (MICRO), type 6 (ENHANCE)
make 'a/E mask Dice coef' parent of 'mask correlation'
28 Oct 2015, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 6 (ENHANCE)
look for dice coef file ae_dice, as well ae_corr
26 Oct 2015, RW Cox, afni Clusterize, level 3 (MAJOR), type 6 (ENHANCE)
Allow user to use multiple (up to 4) Aux datasets for Plot/Save
26 Oct 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
compute TSNR restricted to uncensored TRs
26 Oct 2015, RC Reynolds, afni, level 1 (MICRO), type 5 (MODIFY)
move version to show_AFNI_version and call on -ver
23 Oct 2015, RC Reynolds, afni, level 1 (MICRO), type 5 (MODIFY)
move version output after some text requests
21 Oct 2015, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
added -exec
15 Oct 2015, RW Cox, afni Clusterize, level 1 (MICRO), type 5 (MODIFY)
Switch F-stat from using 1-sided to 2-sided tables.
To keep Chen Gang happy.
15 Oct 2015, RW Cox, afni Clusterize, level 1 (MICRO), type 5 (MODIFY)
Modify linkRbrain stuff to NOT use unseen clusters
14 Oct 2015, RW Cox, afni Clusterize, level 1 (MICRO), type 0 (GENERAL)
Add toggle button to turn individual clusters on/off
Hope it doesn't interfere with something else! It's tricky modifying
the functional overlay.
13 Oct 2015, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 5 (MODIFY)
Finally fixed -clust option to correspond to new 3dClustSim output
That is, 9 NIML files instead of 3.
07 Oct 2015, RW Cox, afni GUI, level 1 (MICRO), type 0 (GENERAL)
Attempt to fix 'crash on re-open controller' problem
Happened when Clusterize was used in A, then B opened, B closed, B
re-opened -- boom. Set deleted FD_bricks to NULL seems to help.
Fingers crossed.
01 Oct 2015, RW Cox, AFNI clusterize, level 1 (MICRO), type 5 (MODIFY)
Made showing linkRbrain button default now
setenv AFNI_LINKRBRAIN NO to turn this button off
28 Sep 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 4 (BUG_FIX)
Use list of ROIs to select subnetwork of analysis for 3dMVM.
Previously, sublist only applied to post hocs, not 3dMVM models.
25 Sep 2015, RC Reynolds, suma, level 1 (MICRO), type 5 (MODIFY)
volume rendering is no longer the default for SUMA_VO_InitSlices
So Do_06_VISdti_SUMA_visual_ex1.tcsh defaults to showing 3 volume slices.
24 Sep 2015, RC Reynolds, vol2surf, level 1 (MICRO), type 6 (ENHANCE)
restrict THD_extract_series error messages (e.g. for RGB datasets)
Requested by P Taylor.
24 Sep 2015, RC Reynolds, ccalc, level 1 (MICRO), type 5 (MODIFY)
make dependency on libmri explicit
Some of these operations are for building on Fedora 22.
24 Sep 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
allow 3dD to proceed with only extra_stim_files
24 Sep 2015, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
inline func with static vars should be static
Fails to link in Fedora 22.
22 Sep 2015, RW Cox, 3dDeconvolve, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_USE_ERROR_FILE = NO turns off creation of 3dDeconvolve.err
18 Sep 2015, P Taylor, @GradFlipTest, level 1 (MICRO), type 5 (MODIFY)
For DWI analysis: just linear fitting of tensor.
Faster 3dDWItoDT usage, only do linear fit.
18 Sep 2015, DR Glen, @DBSproc bug fix, level 2 (MINOR), type 4 (BUG_FIX)
Left-right coordinate flip in @DBSproc script for Silvina Horovitz
16 Sep 2015, RC Reynolds, suma, level 1 (MICRO), type 5 (MODIFY)
w/dglen SUMA_find_any_object: fixed loss of isGraphDset result
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.
11 Sep 2015, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
edt_floatize.c: for NIFTI float->float with scale factors, apply them
Also, fix determination of when to convert.
Thanks to Pengmin (MB) for noting this problem.
11 Sep 2015, RC Reynolds, 3dBandpass, level 1 (MICRO), type 5 (MODIFY)
do not propagate scalars
10 Sep 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fix resulting aligned SurfVol if input is NIFTI
09 Sep 2015, RW Cox, whereami (etc), level 1 (MICRO), type 4 (BUG_FIX)
Fix bug in parsing LinkRbrain output XML file
Problem: fread() of file does not NUL terminate the string -- causes
problems! Simply solved.
Also fixed problem in afni_cluster.c, where peak coords and cmass coords
passed to LinkRbrain were being interchanged.
09 Sep 2015, RW Cox, afni clusterize, level 1 (MICRO), type 6 (ENHANCE)
Add popup chooser for max number linkRbrain clusters
03 Sep 2015, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY)
give REML priority in guessing stats_dset
02 Sep 2015, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
some option vars were being over-written
02 Sep 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
add -errts_dset to gen_ss_review_scripts.py command
02 Sep 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
if rest and REML, use REML errts
01 Sep 2015, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 6 (ENHANCE)
track errts dset, and possibly use it for voxel dims
01 Sep 2015, DR Glen, 3dcalc extreme, absextreme, level 2 (MINOR), type 2 (NEW_OPT)
New extreme and absextreme operators to find extreme values
28 Aug 2015, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
Hack to allow -stim_times_IM to work with times > TMAX
Times > TMAX are ignored. In usual cases, this isn't a problem. But
with IM regression, each time gets a regressor, and times > TMAX produce
all zero regressors -- which is a problem. This hack will cut them off
(at least in some cases).
27 Aug 2015, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
check for R packages via 'rPkgsInstall -pkgs ALL -check'
26 Aug 2015, RC Reynolds, Makefile.ptaylor.INCLUDE, level 1 (MICRO), type 6 (ENHANCE)
put -L.. before $LFLAGS to link local libjpeg
25 Aug 2015, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE)
if initial install, update .cshrc
If initial install (afni not in PATH) and PATH not set in .csrhc,
update path (PATH) and do 'apsearch -afni_help_dir' update in .csrhc.
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.
21 Aug 2015, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
start-of-run fix to -multi_timing_to_event_list offsets
21 Aug 2015, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 6 (ENHANCE)
add more help for 'NOTE: distribution of ISI', including a short script
21 Aug 2015, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 6 (ENHANCE)
move gifti_tool/cifti_tool from EXPROGS to PROGRAM_LIST
Modified 28 Makefiles.
21 Aug 2015, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 6 (ENHANCE)
make cifti_tool
20 Aug 2015, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_isi_pdf and -show_isi_f_pdf
19 Aug 2015, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_missing, to show all missing labels from all files
14 Aug 2015, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
SUMA_CIFTI_2_edset: use 'no suma' version: SUMA_WriteDset_ns
13 Aug 2015, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
megrged cifti-toy branch from Ziad, for viewing CIFTI dataset in suma
12 Aug 2015, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 6 (ENHANCE)
allow for generic/unknown commands via -command (e.g. ls, 3dTcat)
Done for W-L Tseng.
12 Aug 2015, RC Reynolds, @radial_correlate, level 1 (MICRO), type 2 (NEW_OPT)
add -mask option, to apply instead of automask
Done for Giri.
11 Aug 2015, RW Cox, 3dFWHMx, level 2 (MINOR), type 2 (NEW_OPT)
-1difMOD option
Computes the moments of the 1st differences, then estimates the mean and
standard deviation of the smoothness factors, then reports the mean
smoothness adjusted upwards to allow for the fact that 3dClustSim
depends more strongly on bigger smoothness than on smaller smoothness.
For use with single subject tests; probably too conservative for group
analyses.
11 Aug 2015, RW Cox, 3dFWHMx, level 1 (MICRO), type 5 (MODIFY)
Modify -2difMAD option calculations
If smoothness calculation fails using Median Absolute Deviation, retry
with Mean Absolute Deviation.
10 Aug 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 2 (NEW_OPT)
Minor new option: input list of ROIs with file.
For minor convenience.
09 Aug 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed minor bug when GM map has no ROIs/clusters.
No more crashing... Won't produce GM or GMI volumes; message only.
07 Aug 2015, RC Reynolds, model_conv_PRF_6, level 1 (MICRO), type 4 (BUG_FIX)
make everything static, to avoid confusion; proto for conv_set_ref
07 Aug 2015, RC Reynolds, model_conv_PRF, level 1 (MICRO), type 5 (MODIFY)
make everything static, to avoid confusion
07 Aug 2015, RC Reynolds, 3dhistog, level 1 (MICRO), type 2 (NEW_OPT)
add -noempty option, to ignore empty bins
05 Aug 2015, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
if conversion to NIFTI-1 header fails on write, try NIFTI-2
05 Aug 2015, RC Reynolds, nifti_tool, level 1 (MICRO), type 6 (ENHANCE)
apply library updates for potentially writing NIFTI-2
05 Aug 2015, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
add some support for reading Voxel_Bucket datasets into AFNI
That is a type that is currently specific to SUMA.
05 Aug 2015, P Taylor, fat_mvm_prep.py, level 1 (MICRO), type 4 (BUG_FIX)
Micro ~bug fixed for inputting CSV headings.
Now strip off lead/trail whitespace, then replace rest with underscore.
03 Aug 2015, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
added DTYPE_3DTM (3D+timing) ACQUSITION_TYPE
Treats data as per volume, but with slice timing. This is needed for
num_chan>0, but when data does not come in num_chan slices at a time.
03 Aug 2015, RC Reynolds, Dimon1, level 1 (MICRO), type 4 (BUG_FIX)
fixed -drive_afni, -drive_wait and -rt_cmd command lists
03 Aug 2015, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
applied ACQUSITION_TYPE as 3d+timing
Slice timing was lost (by the plugin) in the change to 3d+t ACQ TYPE.
Thanks to H Mandelkow for bringing this up.
31 Jul 2015, RC Reynolds, @FindAfniDsetPath, level 1 (MICRO), type 6 (ENHANCE)
allow full paths to succeeed ; no args gives help
30 Jul 2015, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 4 (BUG_FIX)
check for template existence even given path
Was failing with -init_xform.
29 Jul 2015, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT)
add -nzstdev option
Given a voxel, extract all the values. Throw out those values that are
nonzero. Compute the stdev of the remaining set (assuming at least 2),
with no further processing (no detrending).
29 Jul 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
ANATICOR now works with task analysis, using -regress_reml_exec
Done for R W Cox.
29 Jul 2015, RC Reynolds, gen_ss_reivew_scripts.py, level 1 (MICRO), type 5 (MODIFY)
block any _REMLvar stats dset (was _REMLvar+)
Might get stats*_REMLvar_nods, for example, via 3dREMLfit -dsort_nods.
29 Jul 2015, RC Reynolds, 3dcalc, level 1 (MICRO), type 5 (MODIFY)
clarify error about mis-match in number of volumes
28 Jul 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
ANATICOR now includes zero volumes at censor points
This matches non-ANATICOR and fast ANATICOR cases.
27 Jul 2015, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
-dsort_nods option
When used with -dsort, this option will make 3dREMLfit calculate the
results with the -dsort regressors(s) omitted as well as the results
with the -dsort regressor(s) included -- so the user can compare the
dsort and non-dsort results easily with 1 run of the program. 'nods' ==
'no dsort'. Each nods dataset will have the string '_nods' appended to
the prefix.
27 Jul 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
renamed -regress_WMeL_corr to -regress_make_corr_AIC and default to 'no'
24 Jul 2015, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
GIFTI datasets should have NODE_INDEX list as first DataArray
Thanks to N Oosterhof for pointing this out.
23 Jul 2015, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add -dsort option
Allows the addition of voxel-wise baseline regressors. To test out
ANATICOR applied to task-based FMRI data, for example.
23 Jul 2015, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
allow Graph_Bucket niml.dsets to be read, but just as 1D
22 Jul 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed minor bug when refset has negative values.
No more crashing...
17 Jul 2015, RW Cox, mri_write.c, level 1 (MICRO), type 4 (BUG_FIX)
Make mri_write_1D("stdout:") work correctly
Before you could get filename "stdout:.1D" which is not very useful.
17 Jul 2015, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
Dimon->afni: small TCP buffers cause volumes to be passed slowly
In iochan_recvall, increase nap time only if packets < 4K are recieved.
13 Jul 2015, RC Reynolds, nifti_tool, level 3 (MAJOR), type 6 (ENHANCE)
nifti_tool is now based on NIFTI-2, with many corresponding new options
The old nifti_tool (based on NIFTI-1) is now nifti1_tool.
13 Jul 2015, RC Reynolds, NIFTI-2, level 3 (MAJOR), type 6 (ENHANCE)
added NIFTI-2 support into AFNI
Main source update: nifti/nifti2 tree, then applied it in mostly
thd_niftiread/write.c (plus gifti_io.h, 3ddata.h, mrilib.h).
To compile into all of AFNI edit: Makefile.INCLUDE, SUMA_Makefile_NoDev,
Makefile.avovk.INCLUDE and Makefile.ptaylor.INCLUDE.
13 Jul 2015, RC Reynolds, nifti1_tool, level 2 (MINOR), type 1 (NEW_PROG)
nifti1_tool is the NIFTI-1 version of nifti_tool
11 Jul 2015, RC Reynolds, @diff.files, level 1 (MICRO), type 2 (NEW_OPT)
added -longlist
09 Jul 2015, DR Glen, suma flip colormaps, level 1 (MICRO), type 5 (MODIFY)
Colormaps imported from AFNI are now flipped 'properly'
07 Jul 2015, P Taylor, fat_mat_sel.py, level 2 (MINOR), type 2 (NEW_OPT)
Simple new option to exclude x-axis labels.
They might just be annoying.
06 Jul 2015, DR Glen, RedBlueGreen Colormap, level 1 (MICRO), type 5 (MODIFY)
New RedBlueGreen colormap for afni and suma
01 Jul 2015, RC Reynolds, cifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
reorg and more recur functions
01 Jul 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 0 (GENERAL)
clarified help for -anat_unif_GM
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.
24 Jun 2015, RC Reynolds, afni_xml_tool, level 2 (MINOR), type 2 (NEW_OPT)
afni_xml udpates, and start to afni_xml_tool
22 Jun 2015, RW Cox, 3dvolreg, level 1 (MICRO), type 5 (MODIFY)
Add output of max inter-TR displacement
In addition to the max total displacement (as of old).
18 Jun 2015, RC Reynolds, 3dExtrema, level 2 (MINOR), type 2 (NEW_OPT)
added -nbest
Output -nbest extrema; -quiet does not suppress extrema output.
17 Jun 2015, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added functions for reading from a buffer
16 Jun 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
applied -regress_stim_times_offset to typical timing files
Allows for stim timing offset when copying to stimuli directory.
16 Jun 2015, RC Reynolds, CIFTI, level 2 (MINOR), type 0 (GENERAL)
added initial nifti/cifti tree
15 Jun 2015, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -disp_cext
14 Jun 2015, DR Glen, align_epi_anat.py edge, level 1 (MICRO), type 4 (BUG_FIX)
Fixed broken edge option
12 Jun 2015, RW Cox, plug_L1fit, level 1 (MICRO), type 5 (MODIFY)
Modify Timeseries input to use all columns of file, not just 1st
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
10 Jun 2015, RC Reynolds, auto_warp.py, level 1 (MICRO), type 4 (BUG_FIX)
clear any AFNI_COMPRESSOR variable, so that scripts do not get confused
NIFTI is the default, so avoid script confusion with automatic nii.gz.
In the future, maybe process as AFNI.
10 Jun 2015, RC Reynolds, NIFTI, level 1 (MICRO), type 4 (BUG_FIX)
THD_open_one_dataset: let THD_open_nifti look for alternate files
CHECK_FOR_DATA() requires a file name match, but NIFTI is forgiving.
08 Jun 2015, RC Reynolds, neuro_deconvolve.py, level 1 (MICRO), type 6 (ENHANCE)
allow -inputs to include paths
06 Jun 2015, RC Reynolds, timing_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -per_run_file
05 Jun 2015, RW Cox, 3dSimARMA11, level 1 (MICRO), type 2 (NEW_OPT)
Add hidden -tdof option
02 Jun 2015, RC Reynolds, NIFTI, level 1 (MICRO), type 0 (GENERAL)
NIFTI-1,2: added NIFTI_ECODE_CIFTI/VARIABLE_FRAME_TIMING/EVAL/MATLAB
02 Jun 2015, DR Glen, plugout_drive to stdout or file, level 1 (MICRO), type 3 (NEW_ENV)
Allow plugout_drive to get xyz,ijk,AFNI environment to file
plugout_drive for GET_DICOM_XYZ, GET_ENV was to stdout of afni
GUI. This was difficult to parse. Allow resetting output to file
using AFNI_OUTPLUG environment variable or SET_OUTPLUG command
02 Jun 2015, DR Glen, graph allow single time point for writing graph, level 1 (MICRO), type 5 (MODIFY)
Allow single TR/anat dataset to work with 'w' in graph mode
01 Jun 2015, RC Reynolds, nifti_tool, level 2 (MINOR), type 6 (ENHANCE)
diff/disp_hdr detects type; diff_hdr1/2
01 Jun 2015, RC Reynolds, 3dttest++, level 1 (MICRO), type 2 (NEW_OPT)
added -dupe_ok and more warnings when dataset labels match
27 May 2015, RC Reynolds, @Install_TSrestMovieDemo, level 1 (MICRO), type 4 (BUG_FIX)
set and applied $demo as Suma_TSrestMovieDemo
26 May 2015, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT)
Add secret -tdof option
26 May 2015, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
nifti_read_header returns generic pointer; rename N-1/2 header read funcs
26 May 2015, RC Reynolds, 3dBlurToFWHM, level 1 (MICRO), type 5 (MODIFY)
make -help output consistent in using FWHM (along with 3dLocalstat)
22 May 2015, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
allow for small differences when comparing oblique angles
Define OBLIQ_ANGLE_THRESH=0.01 as a tolerance for the difference.
This was done to fix registration to external dset in realtime.
Thanks to V Roopchansingh for bringing up the problem.
22 May 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
help clarifications for -regress_ROI* options
22 May 2015, DR Glen, 3dLocalstat mode, level 2 (MINOR), type 2 (NEW_OPT)
Find mode and non-zero mode in voxel neighborhood
21 May 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 4 (BUG_FIX)
Minor bug fixed for inputting sublist of ROIs.
Short option for doing so worked, but not the long one; fixed now.
21 May 2015, P Taylor, 3dDWUncert, level 1 (MICRO), type 2 (NEW_OPT)
Can choose to analyze only high-FA voxels: don't waste time on GM/CSF.
Option to ignore low-FA vox for uncert, leave them 0.
19 May 2015, RC Reynolds, 3dClustSim, level 1 (MICRO), type 5 (MODIFY)
do not allow -pthr to preceed -both or -niml
Otherwise -pthr values would be lost.
18 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow ROI PC regression for local masks (not just external ones)
External ROIs should now be passed via -anat_follower_ROI, rather than
-regress_ROI_*, the latter no longer taking dataset parameters.
Also changed -regress_ROI_erode to -anat_follower_erode and
removed option -regress_ROI_maskave (use -regress_ROI)
Done for R W Cox.
18 May 2015, RC Reynolds, gen_ss_review_table.py, level 1 (MICRO), type 2 (NEW_OPT)
mention gen_ss_review_scripts.py -help_fields in help
15 May 2015, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 2 (NEW_OPT)
Can output separate bval file.
Useful in some TORT preprocessing.
14 May 2015, RW Cox, afni Clusterize, level 1 (MICRO), type 5 (MODIFY)
Add ' Detrend?? ' button to hidden popup
Allows user (me) to detrend the aux data before plotting it.
14 May 2015, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
Add -demean option == remove mean from time series before plotting
Multiple -demean options implies higher order polynomials!
12 May 2015, RW Cox, 3dClustSim, level 2 (MINOR), type 5 (MODIFY)
Eliminate edge effects of smoothing by padding and unpadding
Simulate extra-size volumes then smooth, then cut back to the desired
volume size. Can use new '-nopad' option to try the old-fashioned
method. (H/T to Anders Eklund and Tom Nichols.)
08 May 2015, RW Cox, InstaCorr, level 1 (MICRO), type 4 (BUG_FIX)
Change way index in 3D+time dataset is chosen from xyz
Instead of just converting from xyz (eg, crosshair) coordinates via the
standard grid transformation functions in thd_coords.c, what we want is
the voxel in the 3D+time dataset that is closest in 3D to the xyz
location AFTER it is transformed back to the underlay for display. In
this way, the center of correlation will map to the clicked voxel. This
selection is done in new function THD_find_closest_roundtrip() which
searches the 27 points in a cube around the thd_coords.c derived point,
in order to find the voxel in the 3D+time dataset that, when transformed
back to the underlay dataset, is closest. Brute force, but that's what
you have to do when dealing with the Spanish Inquisition.
08 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_make_corr_vols
Use this to compute average correlation volumes for various masks.
07 May 2015, RW Cox, AFNI GUI, level 1 (MICRO), type 5 (MODIFY)
Change 'List of AFNI papers' to be in HTML, not plain text
So it appears in an htmlwin rather than a textwin, and there are links
to the papers. Works by a new convert_text_to_html() function.
07 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
replaced slow 3dTfitter with 3dTproject in anaticor
This should not affect the result, just the processing time.
05 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added help (inc Ex 11), follower modifications, WMe corr diag change
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
04 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -anat_follower, -anat_follower_ROI, -regress_anaticor_label
01 May 2015, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY)
keep num regs of interest = 0 if num stim = 0
30 Apr 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT)
allow AM2 centering param via basis backdoor (for now)
For example, use basis function 'BLOCK(2) :x:0.176'
Done for J Britton.
30 Apr 2015, DR Glen, Selenium webdriver for afni help page too, level 1 (MICRO), type 0 (GENERAL)
Opens page for all afni help page using python selenium webdriver
29 Apr 2015, RC Reynolds, NIFTI, level 2 (MINOR), type 5 (MODIFY)
allow reading and writing unknown extensions
28 Apr 2015, RC Reynolds, NIFTI, level 3 (MAJOR), type 6 (ENHANCE)
apply updates to NIFTI-2 I/O library
Also, include initial mods to nifti_tool, hidden under nifti2 dir.
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
28 Apr 2015, RC Reynolds, NIFTI, level 2 (MINOR), type 0 (GENERAL)
add nifti/nifti2 directory with current NIFTI-1 versions of 4 files
This tracks initial changes to nifti2_io.[ch] nifti_tool.[ch].
28 Apr 2015, DR Glen, to3d - do not write BRIK, level 1 (MICRO), type 2 (NEW_OPT)
Do not write binary data with -nowritebrik
May be useful for faster realtime acquisition with symlinks
27 Apr 2015, RW Cox, debug tracing, level 1 (MICRO), type 0 (GENERAL)
Added 'recent internal history' to .afni.crashlog
The last few ENTRY/EXIT/STATUS updates are saved, to help pinpoint the
sequence of events before the demise of the patient.
27 Apr 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed output when byte/short insets were used.
Had been not writing data; needed to null brick_facs in outsets.
24 Apr 2015, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 6 (ENHANCE)
tiny help update: examples of usage regarding subject IDs
23 Apr 2015, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX)
Fix Aux.Dset button crash in Clusterize
Because Ziad Saad is trouble, that's why.
(Either that, or 'free(x)' should imply 'x=NULL'.)
Also, catch SIGABRT signal, so Mac malloc() errors are tracebacked.
23 Apr 2015, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 2 (NEW_OPT)
add -help_fields[_brief], to describe the 'basic' output fields
22 Apr 2015, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
add fix for non-unix files; allow for multiple tests with -prefix
22 Apr 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
put in cat_matvec string to create warp.all.anat.aff12.1D
Thanks to sgreen (MB) for noting the problem.
22 Apr 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add -todo; help update; verify use of erode list
22 Apr 2015, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
Makefile.linux_fedora_19_64: alter -I dirs for glib to build on F21
15 Apr 2015, ZS Saad, suma-general, level 3 (MAJOR), type 4 (BUG_FIX)
Turned off USE_XOR for now.
Was causing very mysterious problem with labels displaying atop each other
in the SUMA viewer. Possibly other problems too like crash when opening
surface controller or changing threshold. No time to get to the bottom
of this at this time. But turning this off fixed problem on linux and osx.
Valgrind had nothing to complain about...
14 Apr 2015, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX)
Fix index text overlay clash in graph window
Because Daniel Glen is trouble, that's why.
14 Apr 2015, RC Reynolds, uber_subject.py, level 1 (MICRO), type 2 (NEW_OPT)
add MIN_OUTLIERS as an option for volreg base
14 Apr 2015, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 5 (MODIFY)
PLOT_matrix_gray: add error messages to clarify malloc failures
13 Apr 2015, RW Cox, all programs, level 1 (MICRO), type 0 (GENERAL)
AFNI programs now write crash logs to file ~/.afni.crashlog
13 Apr 2015, RW Cox, AFNI itself, level 1 (MICRO), type 4 (BUG_FIX)
Fix crash when ClustSim info in dataset header is incomplete
Problem was if mask string was missing, it tried to read the
mask idcode from a now-deleleted NIML element -- bad news.
09 Apr 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fix -tlrc_NL_warped_dsets for NIFTI anat; add some -regress_ROI_PC help
08 Apr 2015, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
updated to Ziad's new -revert option
08 Apr 2015, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
check for FATCAT_DEMO
07 Apr 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
TLRC_warped_dsets: no view update if type != BRIK
07 Apr 2015, RC Reynolds, afni_base.py, level 1 (MICRO), type 5 (MODIFY)
ppves: no sel -> no quotes; dset_dims: check failures and return 4 vals
07 Apr 2015, RC Reynolds, 3dnvals, level 1 (MICRO), type 5 (MODIFY)
have 3dnvals return status 1 if all dataset opens fail
03 Apr 2015, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Changes to how labeled datasets (volumes in particular) are shown in SUMA
Made atlas and labeled volumes appear in SUMA as they do in AFNI.
No labels show up upon clicking though. Appearance of labeled dataset
will change for labeled datasets created earlier, unless env.
SUMA_Classic_Label_Colors is set to YES
03 Apr 2015, ZS Saad, suma-general, level 1 (MICRO), type 3 (NEW_ENV)
SUMA_Classic_Label_Colors , see .sumarc after updating it for details
02 Apr 2015, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT)
Added ctrl+l and ctrl+L to globally dim/brighten lighting
02 Apr 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -tlrc_NL_warped_dsets to import 3dQwarp result
Added for P Molfese and others.
02 Apr 2015, RC Reynolds, rickr/Makefile, level 1 (MICRO), type 4 (BUG_FIX)
Imon and serial_helper should not use LLIBS
01 Apr 2015, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
anat followers and ROI_PC
Datasets can follow the anatomical warps
Added options -regress_ROI_PC, -regress_ROI_maskave, -regress_ROI_erode.
PC allows for some number of principle components to be regressed, and
maskave is for mask averages to be regressed.
The _erode option applies to either, and happens before xform.
Also, any anat with skull is applied as a follower.
Also, -tcat_remove_first_trs can now take a list.
01 Apr 2015, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 6 (ENHANCE)
allow -censor_fill_parent with 2D files
31 Mar 2015, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 6 (ENHANCE)
allow -censor_fill_parent with simple 1D files
Done for 3dpc and censoring in afni_proc.py.
30 Mar 2015, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
update for selenium
Includes: Makefile.linux_openmp*, xorg7*, osx_10.7*, fedora19_64,
as well as Makefile.INCLUDE and rickr/Makefile for LLIBS.
27 Mar 2015, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Selection now possible on VR rendered image in SUMA
27 Mar 2015, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed syntax for env SUMA_VO_InitSlices, space chars are bad.
27 Mar 2015, RW Cox, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
linux_xorg7_64 distribution gets argv[nopt] wrong?!
Fixed by putting in a debug printout statement for argv[nopt] at start
of loop over options. Even when not used, this fixes the problem --
probably caused by the gcc optimizer.
27 Mar 2015, DR Glen, Selenium webdriver to open webpages, level 3 (MAJOR), type 0 (GENERAL)
Opens webpages without multiple tabs using python selenium webdriver
23 Mar 2015, ZS Saad, BrainSkin, level 2 (MINOR), type 4 (BUG_FIX)
Fixed projection error in SUMA_NN_GeomSmooth?_SO
23 Mar 2015, RW Cox, 3dttest++, level 3 (MAJOR), type 2 (NEW_OPT)
Add -singletonA option
For testing one subject vs a collection of 'normals'. Works with
covariates.
23 Mar 2015, RC Reynolds, python-general, level 2 (MINOR), type 6 (ENHANCE)
broke VarsObject class out into separate file
19 Mar 2015, RC Reynolds, unix_tutorial, level 2 (MINOR), type 6 (ENHANCE)
populated AFNI_data6/unix_tutorial with Sphinx version
The previous tutorial was moved under 'old'.
18 Mar 2015, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Node depths were being computed along the principal direction closest to Z
The proper intent is along the principal direction, regardless of
whether or not it is closest to the Z direction
18 Mar 2015, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added -node_depth
18 Mar 2015, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Added options -in_range, -ex_range for thresholding and output COM and Cent
These changes resulted in numerous small changes throughout the code for
a more uniform handling of thresholding methods
18 Mar 2015, RC Reynolds, sphinx, level 3 (MAJOR), type 6 (ENHANCE)
added unix_tutorial to the doc tree
18 Mar 2015, RC Reynolds, sphinx, level 1 (MICRO), type 5 (MODIFY)
renamed tutorials.rst to SelfGuidedScripts.rst, along with tag
18 Mar 2015, RC Reynolds, 3dBandpass, level 1 (MICRO), type 6 (ENHANCE)
let user know details of demensionality reduction
13 Mar 2015, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT)
Added ExistsAs in ParseName
This can find whether or not you have datasets on disk with some
view (+tlrc), say given only a prefix.
13 Mar 2015, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
added code to receive and store ECHO_TIMES
This is passed as control information and is stored in rtin->TE.
13 Mar 2015, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
added V Roopchansingh update for T2* est Merge function
13 Mar 2015, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT)
added option -te_list to pass ECHO_TIMES to plug_realtime
12 Mar 2015, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
Added -pc* and -key options to compute coordinate PC of clusters.
See -help for details.
12 Mar 2015, RC Reynolds, afni_util.py, level 1 (MICRO), type 6 (ENHANCE)
implemented fast=0 in get/show_process_stack
12 Mar 2015, RC Reynolds, afni_base.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed capture in shell_exec2 for old python, where readlines() would hang
12 Mar 2015, RC Reynolds, 3dDeconvolve.py, level 1 (MICRO), type 5 (MODIFY)
allow for collinearity in regressor warnings
11 Mar 2015, ZS Saad, 3dSeg, level 3 (MAJOR), type 2 (NEW_OPT)
Added -mixfloor to avoid getting NAN when certain classes disappear.
Also added -mixfrac IGNORE to turn off any modulation by the mixing
fraction during the EM routines.
11 Mar 2015, RW Cox, afni GUI, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_CROSSHAIR_THICKNESS
Lets user set thickness of image crosshair lines. For someone named
Corianne, if that is a real name.
11 Mar 2015, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
added covary and linear_fit; -listfunc takes -/stdin to read from stdin
auto-generated by afni_history on Sep 4 2009