AFNI HISTORY
level 2 and higher
The levels of importance go from 1 to 5, with meanings:
1 - users would not care
2 - of little importance, though some users might care
3 - fairly important
4 - a big change or new program
5 - IMPORTANT: we expect users to know
generated via the command : afni_history -html -reverse -min_level 2 -past_years 2
---- log of AFNI updates (most recent first) ----
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.
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.
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.
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.
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
01 Feb 2017, RC Reynolds, afni_system_check, level 2 (MINOR), type 6 (ENHANCE)
updates for fink and homebrew
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.
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.
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
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.
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
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
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.
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.
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.
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.
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.
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.
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, 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, 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.
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.
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)
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
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
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, 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.
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.
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.
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)
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
05 Aug 2016, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -marry_AM
Added for J Wiggins.
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.
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
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, DR Glen, align_epi_anat.py flipping identity, level 2 (MINOR), type 4 (BUG_FIX)
Case of mistaken IDENTITY for check_flip option
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
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.
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?
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, 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, 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
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, 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, 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
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.
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.
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.
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.
27 Apr 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
prep for later: always extract volreg base, as vr_base*
19 Apr 2016, DR Glen, unWarpEPI.py, level 2 (MINOR), type 1 (NEW_PROG)
blip-up/down distortion correction script
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, 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.
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.
25 Mar 2016, RW Cox, afni GUI, level 2 (MINOR), type 2 (NEW_OPT)
A bunch of '-XXX' options to control colors and fonts
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.
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).
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
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.
19 Feb 2016, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
add many tests and summarize potential issues
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!
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.
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, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
rigid_body alignment option and better handling of user allineate options
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.
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 .
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.
08 Dec 2015, RW Cox, afni Clusterize, level 2 (MINOR), type 5 (MODIFY)
Add Write button to save just one cluster to a dataset
07 Dec 2015, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT)
Add -resid option, to save residuals.
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.
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.
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
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
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.
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, 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.
01 Sep 2015, DR Glen, 3dcalc extreme, absextreme, level 2 (MINOR), type 2 (NEW_OPT)
New extreme and absextreme operators to find extreme values
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.
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
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.
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.
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.
05 Aug 2015, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
if conversion to NIFTI-1 header fails on write, try NIFTI-2
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.
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.
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.
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.
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, 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
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.
01 Jul 2015, RC Reynolds, cifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
reorg and more recur functions
24 Jun 2015, RC Reynolds, afni_xml_tool, level 2 (MINOR), type 2 (NEW_OPT)
afni_xml udpates, and start to afni_xml_tool
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
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
01 Jun 2015, RC Reynolds, nifti_tool, level 2 (MINOR), type 6 (ENHANCE)
diff/disp_hdr detects type; diff_hdr1/2
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
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, 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.
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.
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.
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, 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, 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
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].
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.
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
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...
08 Apr 2015, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
updated to Ziad's new -revert option
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
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.
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.
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, 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
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
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.
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, 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