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_months 6
---- log of AFNI updates (most recent first) ----
18 Jul 2008, RC Reynolds, 3dNLfim, level 2 (MINOR), type 5 (MODIFY)
listed signal and noise models in -help output
18 Jul 2008, DR Glen, to3d, level 2 (MINOR), type 5 (MODIFY)
Reverse order of slices in Siemens Mosaic data
Some Siemens Mosaic data can be in reverse order depending upon
obscure Siemens private DICOM tags.
Thanks to Doug Greve in Freesurfer group for edifying this situation
17 Jul 2008, RC Reynolds, 3dNLfim, level 2 (MINOR), type 5 (MODIFY)
warn the user if DSET_NVALS is not the same as DSET_NUMTIMES
That would suggest the dataset has no time axis.
16 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added -disp_all to give formatted display of 'all' mask data
This was added for P Kundu.
16 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added choice of 'Vals to Send' to serial_helper
Can now send index,i,j,k,x,y,z,value for every value in mask.
15 Jul 2008, RW Cox, count, level 1 (MICRO), type 4 (BUG_FIX)
Make '-suffix' work correctly for last item (per Fred Tam).
Also, make '-sep' and '-suffix' work as separate items,
instead of as synonyms for the same thing, which is stoopid.
15 Jul 2008, DR Glen, general, level 2 (MINOR), type 5 (MODIFY)
Can turn off all obliquity warnings
AFNI_NO_OBLIQUE_WARNING variable is extended to turn off warnings
about using oblique data in commandline programs and in GUI
15 Jul 2008, DR Glen, 3dWarp, level 2 (MINOR), type 4 (BUG_FIX)
Print correct obliquity transformation matrix
14 Jul 2008, RW Cox, 3dDeconvolve, level 1 (MICRO), type 5 (MODIFY)
Add 'RunStart' field to xmat.1D output, to indicate start of runs.
14 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
terminate TCP transmission to serial_helper if mask is bad
14 Jul 2008, RC Reynolds, afni_history, level 2 (MINOR), type 5 (MODIFY)
a single integer option is interpreted as with -past_entires
14 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -sleep_init, -sleep_vol, -sleep_frac
These options control the timeout periods between data checks.
11 Jul 2008, RC Reynolds, Dimon, level 1 (MICRO), type 5 (MODIFY)
include last 4 elements of obl_matrix, even though probably useless
10 Jul 2008, RC Reynolds, plug_realtime, level 3 (MAJOR), type 5 (MODIFY)
receive oblique transform matrix via new OBLIQUE_XFORM interface
10 Jul 2008, RC Reynolds, Dimon, level 3 (MAJOR), type 5 (MODIFY)
if the data is oblique, pass the transformation matrix to plug_realtime
09 Jul 2008, RC Reynolds, plug_realtime, level 1 (MICRO), type 5 (MODIFY)
if user closes graph window, allow comm with serial_helper to proceed
07 Jul 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
move extra newline from args_as_command to show_args_as_command
03 Jul 2008, RW Cox, matrix.c, level 1 (MICRO), type 5 (MODIFY)
Add QR function matrix_qrr() to matrix.c library file.
03 Jul 2008, RC Reynolds, plug_drawdset, level 1 (MICRO), type 4 (BUG_FIX)
edt_dset_items.c: for .hdr, use .img brick file, storage_mode = BY_NIFTI
02 Jul 2008, RC Reynolds, Dimon, level 1 (MICRO), type 5 (MODIFY)
provide suggestions in the case of a real-time TCP connection failure
01 Jul 2008, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
fixed crash in case of mosaic and un16, no longer having im data
Problem found by R. McColl.
01 Jul 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
modified the make system for building programs in the install directory
- modified Makefile.INCLUDE's INFLAGS and ISFLAGS
- modified SUMA_INPATH in SUMA_Makefile_NoDev.
- removed 'rickr/' dirs from includes in mrilib.h, plug_crender.c and
3dAllineate.c
Requested by V. Roopchansingh of MCW.
30 Jun 2008, RC Reynolds, gen_epi_review.py, level 2 (MINOR), type 5 (MODIFY)
make script executable, decrease sleep, add usage comment in script
30 Jun 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -gen_epi_review and -no_epi_review options
By default, a drive_afni script to review EPI data is now generated.
27 Jun 2008, RC Reynolds, gen_epi_review.py, level 3 (MAJOR), type 1 (NEW_PROG)
generate afni/drive_afni script to review initial EPI data
This program was written to be called from the afni_proc.py output script.
27 Jun 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
small modification to find_command_end
25 Jun 2008, RC Reynolds, howto, level 2 (MINOR), type 5 (MODIFY)
put disclaimers at the tops of HowTo #1, #2, and #5
references to current AFNI class handouts were included
25 Jun 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -past_entries option
24 Jun 2008, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Extend max number of clusters reportable, for Shruti.
24 Jun 2008, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
added the ability to output 1D iresp datasets
20 Jun 2008, RC Reynolds, libmri, level 2 (MINOR), type 5 (MODIFY)
thd_niftiread: do not scale to float if scale=1 and inter=0
19 Jun 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 5 (MODIFY)
help update, added -show_valid_opts, use '*' as separator w/amplitudes
19 Jun 2008, RC Reynolds, file_tool, level 1 (MICRO), type 5 (MODIFY)
removed printing of pointers in disp_ functions
18 Jun 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixes - duplicate master options, mislabeled variable
16 Jun 2008, RC Reynolds, file_tool, level 2 (MINOR), type 5 (MODIFY)
show output for multiple bad files when using -show_bad_backslash
13 Jun 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 2 (NEW_OPT)
added nifti_compiled_with_zlib()
13 Jun 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -with_zlib, and ability to add extensions via 'file:FILENAME'
extension update added for J. Gunter
13 Jun 2008, RC Reynolds, 3dclust, level 2 (MINOR), type 5 (MODIFY)
in the help, Volume defaults to microliters, unless -dxyz=1 is used
12 Jun 2008, RC Reynolds, neuro_deconvolve.py, level 2 (MINOR), type 1 (NEW_PROG)
generate 3dTfitter script to deconvolve a BOLD signal into a neuro signal
12 Jun 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
added get_dset_reps_tr, get_default_polort, get_dset_reps_tr, max_dim_1D
also, updated find_last_space to deal with long strings
12 Jun 2008, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
shifted code to afni_util.get_dset_reps_tr and .get_default_polort
11 Jun 2008, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 5 (MODIFY)
Obliquity handling in alignment, more grid options
11 Jun 2008, DR Glen, afni_base.py, level 1 (MICRO), type 5 (MODIFY)
Added isFloat method to python support
11 Jun 2008, DR Glen, 3dWarp.c, level 1 (MICRO), type 5 (MODIFY)
Prints oblique transformation matrix
10 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 2 (NEW_OPT)
Add -ARMA option to estimate ARMA(1,1) parameters
06 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation matrix of a time series, averaged locally.
06 Jun 2008, RW Cox, 3dErrtsCormat, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation matrix of a time series, globally.
06 Jun 2008, RC Reynolds, plug_crender, level 2 (MINOR), type 4 (BUG_FIX)
integral threshold was off by 1
06 Jun 2008, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 5 (MODIFY)
get_*_opt now returns an error code
03 Jun 2008, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Made AFNI_IMAGE_TICK_DIV_IN_MM editable (in 'Edit Environment')
This is Rick's method for putting a physical scale around the edge of an
image. Of course, you have to use the grayscale intensity bar popup
menu to actually put the tick marks on. This just converts the
'division' count to mm.
02 Jun 2008, RC Reynolds, model_demri_3, level 1 (MICRO), type 5 (MODIFY)
small help update to clarify residual C curve input
02 Jun 2008, RC Reynolds, GIFTI, level 1 (MICRO), type 0 (GENERAL)
added CMakeLists.txt and XMLCALL update from Simon Warfield
also added LICENSE.gifti
29 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 5 (MODIFY)
allowed for -polort -1 and for sub-brick selection with dataset names
29 May 2008, RC Reynolds, model_demri_3, level 1 (MICRO), type 4 (BUG_FIX)
help update to clarify use of AFNI_MODEL_D3_R1I_DSET
22 May 2008, RC Reynolds, 3dTshift, level 2 (MINOR), type 4 (BUG_FIX)
with -rlt, slices without any time shift must still be processed
problem noticed by Jie Huang
21 May 2008, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Put -1dindex into '3dclust' output from Clusterize report. Oops.
21 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed incorrect scaling in Cp computation
The error was introduced on April 8, 2008.
21 May 2008, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 2 (NEW_OPT)
added -amplitudes option (for Rutvik Desai)
20 May 2008, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
Clusterize: '-' as the filename means write to stdout.
20 May 2008, RW Cox, plugout_drive, level 1 (MICRO), type 2 (NEW_OPT)
Make TCP/IP to 'localhost' the default. Add option '-shm' if needed.
20 May 2008, RW Cox, afni_cluster.c, level 1 (MICRO), type 0 (GENERAL)
Added BHelp to a bunch of buttons.
18 May 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added options for TR-locking and storing '3dDeconvolve -nodata' examples
- added shuffle() to replace that from random (cannot produce all perms)
- added options -tr, -tr_locked and -save_3dd_cmd
- changed -stim_time option to -stim_dur
18 May 2008, RC Reynolds, afni_history, level 1 (MICRO), type 5 (MODIFY)
sped up comparison (since histories have gotten long)
17 May 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
check result of 3dDeconvolve execution in output script
If 3dDeconvolve fails, terminate the script so that the user can
see what happened.
15 May 2008, ZS Saad, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
added -n_rand and -n_randseed
15 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 4 (BUG_FIX)
Fixed memory corruption when using more than 20 regressors
15 May 2008, RW Cox, thd_initdblk.c, level 1 (MICRO), type 3 (NEW_ENV)
AFNI_IGNORE_BRICK_FLTFAC = YES means ignore brick factors on input
This is a quick hack for Ziad, and must be used with care! Example:
3dBrickStat -DAFNI_IGNORE_BRICK_FLTFAC=YES -max -slow fred+orig
14 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed application of decay term
14 May 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
1D file names for child epi data,micro changes
13 May 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -set_extern_filelist option, and help for using external data files
13 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
gifticlib-1.0.0: initial release
includes support for (set/clear/read/write) external data files
09 May 2008, ZS Saad, 3dROIstats, level 3 (MAJOR), type 2 (NEW_OPT)
Added option -1Dformat to output results in 1D format
09 May 2008, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Modify PUTENV macro to malloc new string for each variable
Previously used an array str[256] that would go away, and that's
actually not legal in Linux -- the array must be permanent, since its
pointer is what gets put in the environment, not a copy of the string.
That's why the PUTENV didn't work on Linux (but worked for some reason
on Mac OS X)! Sheesh.
09 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
gifticlib-0.0.18: giiCoordSystem is now an array of struct pointers
modified GIFTI library, along with suma_gifti.c
08 May 2008, ZS Saad, 3dsvm, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed memory corruption caused by improper declaration of combName
08 May 2008, RW Cox, edt_dsetitems.c, level 1 (MICRO), type 0 (GENERAL)
new prefix *.hdr gets a 2-file NIfTI format output
08 May 2008, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL)
Add 'u' or 'o' marker in titlebar to indicate what's the grayscale
08 May 2008, RW Cox, ROI drawing plugin, level 1 (MICRO), type 0 (GENERAL)
Change info label to show BRIK filename rather than dataset prefix
08 May 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL)
small changes to bilinear optimization parameters
08 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 5 (MODIFY)
updated help, NFIRST does not need to imply injection time
07 May 2008, RC Reynolds, make_random_timing.py, level 3 (MAJOR), type 1 (NEW_PROG)
generate random stimulus timing files
This generates random timing files suitable for use in 3dDeconvolve.
The timing is not restricted to a TR grid, though that is possible.
Consider use with '3dDeconvolve -nodata'.
07 May 2008, RC Reynolds, plug_3Ddump_V2, level 2 (MINOR), type 4 (BUG_FIX)
allow 4D datasets to be opened (so that buckets are again usable)
PLUGIN_dset_check() now checks NVALS instead of NUM_TIMES...
07 May 2008, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT)
added get_type_list and other accessor functions
02 May 2008, RW Cox, mcw_glob.c, level 1 (MICRO), type 0 (GENERAL)
added message from Graham Wideman when readdir() fails
01 May 2008, RW Cox, afni_cluster.c, level 1 (MICRO), type 0 (GENERAL)
Add SaveMask button to Clusterize report window.
Saves the clusters as a mask dataset (cluster #1 has value=1, etc.).
Uses the prefix in the text field for the dataset name -- will overwrite
existing dataset if the same name is used twice. Equivalent 3dclust
command is saved in History Note in output mask dataset (as if you had
pressed the '3dclust' button).
01 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
treat RESID_CT as Ct(t), not C(t)
30 Apr 2008, RW Cox, mcw_glob.c, level 2 (MINOR), type 3 (NEW_ENV)
setenv AFNI_SHELL_GLOB YES == wildcard expansion via the shell
For Graham Wideman and Mac OS X Server 10.5 problems.
30 Apr 2008, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 4 (BUG_FIX)
replaced make_stim_files with make_stim_times.py in help
24 Apr 2008, ZS Saad, SurfSmooth, level 1 (MICRO), type 4 (BUG_FIX)
Fixed leaky SurfSmooth.
Leak was from one of fin_float pointers in Head07
Also found leak in THD_extract_detrended_array and a few
more small leaks in other SUMA function. Valgrind is good.
23 Apr 2008, ZS Saad, afni-python, level 1 (MICRO), type 5 (MODIFY)
Changed methods in afni_name class
.path is now absolute
.inp() and .out() should be used to specify input and output volumes
Updated lpc_align.py and align_epi_anat.py to reflect changes.
17 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor changes
Child epi datasets can be volume registered even if parent epi
is a single sub-brick
16 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
multiple changes
Naming conventions for tlrc output, generic shell compatible,
regridding options for epi and tlrc epi output
14 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
minor change
3dAllineate options are also applied to epi to anat alignment,
so output EPI datasets get original resolution and type.
10 Apr 2008, RC Reynolds, afni_proc.py, level 1 (MICRO), type 0 (GENERAL)
updated the -help with information regarding runs of different lengths
10 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor changes
remove tabs in file, change output file names for epi children,
changes to help, and renamed tlrc parent option
08 Apr 2008, RW Cox, 3dUpsample, level 2 (MINOR), type 1 (NEW_PROG)
Upsample a 3D+time dataset (in the time direction)
08 Apr 2008, RW Cox, 3dTfitter, level 1 (MICRO), type 4 (BUG_FIX)
Deal with ref (LHS) vectors that are very tiny.
Modify thd_fitter.c so that ref vectors that are very tiny compared to
the largest one will not be included in the regression. Per the
unreasonable request of Rasmus Birn.
08 Apr 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 4 (BUG_FIX)
Weighting in LPC cost function
Realized that weighting in computing the LPC was only done on the blok
level computation of the PC. All the blok PC values were averaged
together without weighting. Modified code to use sum of weights over a
blok as a weight for its PC. This can be turned off by setting
environment variable AFNI_LPC_UNWTBLOK to YES (to restore the LPC
function to its previous behavior).
08 Apr 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 3 (NEW_ENV)
allow residual Ct values via AFNI_MODEL_D3_RESID_CT_DSET dataset
e.g. setenv AFNI_MODEL_D3_RESID_CT_DSET residual_Ct+orig
08 Apr 2008, RC Reynolds, 2dImReg, level 2 (MINOR), type 4 (BUG_FIX)
allow zero slices, passing input as result
Choleski factorization would fail on an empty slice. In this case,
return the input slices as the result (instead of crashing).
Done with D Glen.
08 Apr 2008, RC Reynolds, 3dNLfim, level 1 (MICRO), type 5 (MODIFY)
only update output every 100 voxels
07 Apr 2008, RW Cox, 1dUpsample, level 2 (MINOR), type 1 (NEW_PROG)
Upsample a 1D time series
07 Apr 2008, DR Glen, align_epi_anat.py, level 4 (SUPER), type 1 (NEW_PROG)
Alignment of EPI and Anatomical datasets
Aligns anat and EPI data. Alignment is in either direction of anat to
epi or epi to anat. Transformations are combined where possible as
from time series registration and talairach transformations. Multiple
child epi datasets may be aligned at the same time.
04 Apr 2008, RW Cox, 3dAllineate, level 2 (MINOR), type 0 (GENERAL)
Added '-nwarp bilinear' option
Experimental nonlinear warping comes to 3dAllineate at last.
Preliminary test looks good, but more work is needed to be sure it's OK.
04 Apr 2008, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL)
Check for ' ' option, which means a blank after a '\' character
02 Apr 2008, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Changed suma -environment's output to reflect user's current environment.
With this change, users can always replace their .sumarc with
the one output by suma -environment without worrying about loosing
their preferred settings.
02 Apr 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
extended maximum number of contrasts to 75
01 Apr 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
increased internal memory for 3dbucket and 3drefit command creation
31 Mar 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
extended maximum number of means, diffs and contrasts to 50
28 Mar 2008, RW Cox, 3dcalc, level 1 (MICRO), type 5 (MODIFY)
Treat auto-transposed .1D\' files as datasets, not as timeseries.
28 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -copy_gifti_meta and -copy_DA_meta options
28 Mar 2008, RC Reynolds, gifticlib, level 1 (MICRO), type 2 (NEW_OPT)
added routines to copy MetaData
28 Mar 2008, DR Glen, 3dDTeig, level 2 (MINOR), type 4 (BUG_FIX)
small negative eigenvalues are set to zero as in 3dDWItoDT
This fix avoids FA being set to 0 for those affected voxels
27 Mar 2008, ZS Saad, afni-matlab, level 2 (MINOR), type 5 (MODIFY)
Added other return options for Read_1D.m and BrikLoad.m
27 Mar 2008, ZS Saad, suma-general, level 1 (MICRO), type 5 (MODIFY)
Changed internal handling of various MATVEC sources.
Simplified handling of different sources of MATVECs from
AFNI's headers. Added handling of ALLINEATE_MATVEC to the
mix.
26 Mar 2008, ZS Saad, cat_matvec, level 2 (MINOR), type 5 (MODIFY)
cat_matvec can now output IJK_TO_CARD_DICOM and IJK_TO_DICOM_REAL
26 Mar 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -align_centers as an option to deal with very large moves
It used to be that users had to run @Align_Centers on all their
data when big moves were needed to align the surface's antaomy
to that of the experiment. This is no longer needed.
26 Mar 2008, ZS Saad, @Align_Centers, level 2 (MINOR), type 5 (MODIFY)
Script now outputs a matrix that represents the shift
This matrix can be used with 3dAllineate to perform the shift.
26 Mar 2008, ZS Saad, 3dvolreg, level 2 (MINOR), type 4 (BUG_FIX)
3dvolreg's -1Dmatrix_save was not always accounting for centers of rotation
Now the output of -1Dmatrix_save always matches what one would get for
the first sub-brick from
cat_matvec FRED+orig::VOLREG_MATVEC_000000 -I
26 Mar 2008, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
Add -norm2 and -normx options: normalize time series before plotting
26 Mar 2008, RC Reynolds, gifticlib, level 1 (MICRO), type 5 (MODIFY)
in compare, if comp_data is not set, state the fact
26 Mar 2008, DR Glen, python, level 2 (MINOR), type 4 (BUG_FIX)
repaired support for dry_run mode in python scripts
26 Mar 2008, DR Glen, matrix.c, level 1 (MICRO), type 4 (BUG_FIX)
freed matrix used in matrix_sqrt functions
25 Mar 2008, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Instead of SAME, one can use surface's name as LocalDomainParent
25 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
ROIs drawn on different surfaces now handled properly
25 Mar 2008, ZS Saad, ConvertSurface, level 1 (MICRO), type 2 (NEW_OPT)
Added option -ixmat_1D to apply inverse of affine transform
25 Mar 2008, ZS Saad, @auto_tlrc, level 1 (MICRO), type 5 (MODIFY)
Improvements on -rigid_equiv output and .1D transform output
25 Mar 2008, ZS Saad, @SUMA_AlignToExperiment, level 1 (MICRO), type 5 (MODIFY)
View is now changed even if rigid-body registration is used.
25 Mar 2008, RW Cox, 3dDetrend, level 2 (MINOR), type 4 (BUG_FIX)
-normalize didn't work -- what the hellll was I thinking?
Also, added some help to explain how to use 3dDetrend on 1D files.
25 Mar 2008, RW Cox, 1dnorm, level 2 (MINOR), type 4 (BUG_FIX)
Forgot the sqrt()! kudos to David Perlman.
25 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 5 (MODIFY)
the -compare_data option is not separate from -compare_gifti
25 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
minor changes:
- NIFTI_INTENT_NONE is considered valid
- added compare_gifti_data functions
- LabelTables are now written using CDATA
24 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 5 (MODIFY)
deconvolution with penalty factor = 0 is modified
Now the criterion for choosing the penalty factor is based on curvature
rather than distance from the origin. Seems to be more robust, but
probably will require yet more tweaking.
24 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added GERT_Reco options (request of D Glen)
-gert_filename : specify a name for the GERT_Reco script
-gert_nz : override nz=1 in mosaic image files
-gert_to3d_prefix : specify a dataset prefix for the to3d command
24 Mar 2008, RC Reynolds, @Align_Centers, level 2 (MINOR), type 4 (BUG_FIX)
applied proper follower dataset orientation and floating point shifts
The shift applied to the child datasets was based on the parent's
orientation. The shifts were also being truncated to integers.
Changed with D Glen.
21 Mar 2008, ZS Saad, 3dnvals, level 1 (MICRO), type 2 (NEW_OPT)
Added -all to 3dnvals to output all 4 dimensions.
21 Mar 2008, RW Cox, 3dTfitter, level 1 (MICRO), type 5 (MODIFY)
Modified operation of FALTUNG penalty=0 option
Implemented the L-curve method for selecting the penalty factor, when
user sets the factor to 0.
20 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
Add -polort option, to keep Gang Chen happy.
20 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_WRITE_1D_AS_PREFIX allows writing 1D or surface data given the prefix
For example, setting this to YES will allow writing surface data to NIfTI.
18 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -compare_gifti option
See 'gifti_tool -help' for details, including example #7.
18 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added comparison functions to gifticlib
17 Mar 2008, ZS Saad, lpc_align.py, level 1 (MICRO), type 2 (NEW_OPT)
Added -big_move and -partial_coverage.
-big_move is for when large displacements are needed for alignment.
-partial_coverage is for when EPI covers a portion of the brain.
17 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if 1 volume, GERT_Reco_dicom does not give (useless) timing to to3d
14 Mar 2008, RW Cox, 3dROIstats, level 1 (MICRO), type 2 (NEW_OPT)
Sub-brick label printing (and -nobriklab option)
Per the noble Vince Hradil.
13 Mar 2008, RC Reynolds, 3dmerge, level 2 (MINOR), type 0 (GENERAL)
added some examples to the -help output
12 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Changed surface controller font to 8.
You can get the old font size with environment
variable SUMA_SurfContFontSize BIG.
The default is now SMALL.
12 Mar 2008, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Changed crash in SurfaceMetrics when -spec and -i options are mixed.
11 Mar 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 2 (NEW_OPT)
added control of hematocrit via AFNI_MODEL_D3_HCT
10 Mar 2008, RC Reynolds, SUMA_SurfMeasures, level 3 (MAJOR), type 4 (BUG_FIX)
averages did not include nodes lost to -cmask
Noticed by M Beauchamp.
10 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_GIFTI_VERB sets the verbose level in the gifti I/O library
The default is 1, 0 is quiet, and values go up to 7.
10 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 0 (GENERAL)
AFNI can read/write .gii.dset as with .gii
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
applied -gert_outdir in the case of dicom images
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if only 1 run, GERT_Reco_dicom is named per run
07 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Color map in surface controller can be flipped and rotated
* f key for flipping colormap
* Up/Down keys for rotating color map
* Home for home
Hit ctrl+h on Surface Controller's colormap for more help.
07 Mar 2008, RW Cox, Dataset#N, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_DATASETN_NMAX sets number of datasets allowed
New environment variable AFNI_DATASETN_NMAX sets the number of datasets
allowed in Dataset#N plugin, from 9..49. This is for Shruti.
07 Mar 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 4 (BUG_FIX)
properly ignore empty lines, and exit on short files
06 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Added three variables affecting the surface controller
* SUMA_ShowOneOnly: Sets '1 Only' on or off. On by default
* SUMA_GraphHidden: Update open graphs even if corresponding dset
is hidden.* SUMA_ColorMapRotationFraction: Fraction of
colormap to rotate
up or down with arrow keys.
See suma -environment for a complete list.
06 Mar 2008, RW Cox, 3dcalc, level 1 (MICRO), type 5 (MODIFY)
Add cbrt (cube root) function to parser; affects 1deval and ccalc
06 Mar 2008, RC Reynolds, GIFTI, level 1 (MICRO), type 5 (MODIFY)
allow functional control over GIFTI encoding
05 Mar 2008, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
Support for GIFTI surface format writing
GIFTI writing can now be done with SUMA programs.
For example, see options -o_gii and -xml* in ConvertSurface program.
05 Mar 2008, RW Cox, afni-general, level 2 (MINOR), type 5 (MODIFY)
Change the way 1D datasets are written to disk from 3D programs
In programs that analyze time series files (such as 3dTfitter), you can
input 1D files and make the column direction be the time axis by using
suffixing the file with \' -- but when it comes to writing the results
dataset out, the standard AFNI I/O method is to write the time axis
along the row direction. With this change, if you input a 1D file in
the place of a 3D dataset AND put '.1D' at the end of the output file
prefix, then the output dataset will be written so that the time axis
is along the column direction.
05 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
added '-fitts' option to produce fitted time series dataset
05 Mar 2008, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY)
Added 'AFNI History' button to the Datamode->Misc menu
05 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixed passing of INDEX_LIST
05 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
do not duplicate data when reading and writing GIFTI from AFNI
04 Mar 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
couple of small changes to help the hapless users
* add more informative error message if allocate_memory() fails
* force '-float' if any output prefix is NIfTI-1 format (.nii)
04 Mar 2008, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
added -accumulate option, to output each partial sum
for k = 0..N-1 : output[k] = sum(input[i]) over i = 0..k
03 Mar 2008, RW Cox, ++AFNI_History++ plugin, level 1 (MICRO), type 2 (NEW_OPT)
Small changes to make onscreen wordwrap match printout wordwrap
03 Mar 2008, RC Reynolds, website, level 2 (MINOR), type 5 (MODIFY)
updated the AFNI History website pages, with a table of entries
01 Mar 2008, RW Cox, ++AFNI_History++ plugin, level 1 (MICRO), type 1 (NEW_PROG)
Provides a way to create and insert entries into afni_history_NAME.c
User must set two environment variables:
AFNI_HISTORY_PERSONAL_FILE = full path to your personal version of
afni_history_NAME.c
AFNI_HISTORY_USERNAME = what you want for the username in your file
My values of these are
AFNI_HISTORY_PERSONAL_FILE = /Users/rwcox/AFNI/src/afni_history_rwcox.c
AFNI_HISTORY_USERNAME = RWC
You also need to add one of two lines to your afni_history_NAME.c file:
/*=====below THIS LINE=====*/
or
/*=====above THIS LINE=====*/
as shown, with no blanks before or after on the same line (except that
you must make 'BELOW' or 'ABOVE' all caps!).
New history entries are placed below the 'BELOW' line (if present), or
above the 'ABOVE' line.
If you set AFNI_HISTORY_DONTSAVE to YES, then the afni_history_NAME.c
file won't be edited, and the new entry is just written to stdout.
29 Feb 2008, RW Cox, afni_history, level 1 (MICRO), type 0 (GENERAL)
with HTML output, put a rule between different dates
29 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added a TYPE, -type, a new level, and a string to identify each level
29 Feb 2008, G Chen, 3dICA.R, level 4 (SUPER), type 1 (NEW_PROG)
An R program that runs independent component analysis in AFNI.
This testing program for ICA only takes one dataset that presumably has
already been properly pre-processed. See more details on:
http://afni.nimh.nih.gov/sscc/gangc/ica.html
28 Feb 2008, ZS Saad, suma-general, level 3 (MAJOR), type 3 (NEW_ENV)
Support for GIFTI surface format reading
28 Feb 2008, RW Cox, 3dUndump, level 2 (MINOR), type 0 (GENERAL)
allow input of NO text files, to produce an 'empty' dataset
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow constraints on sign of deconvolved function
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow combination of penalty functions in deconvolution
28 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -list_authors option and adjusted spacing
27 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Addition of p and q values under threshold bar
Use BHelp on p and q text in suma to get more info.
27 Feb 2008, ZS Saad, suma-general, level 1 (MICRO), type 4 (BUG_FIX)
Another bout of initialization and leak fixes based on valgrind's output
The hope is that some weird X behavior is caused by uninitialized
variables.
27 Feb 2008, RW Cox, 3dTfitter, level 3 (MAJOR), type 2 (NEW_OPT)
add deconvolution via the '-FALTUNG' option
Unlike 3dDeconvolve, this deconvolution is to find the input time
series, given the impulse response function.
27 Feb 2008, RC Reynolds, afni_history, level 4 (SUPER), type 1 (NEW_PROG)
program to display the history of AFNI updates
This will be used to create a web page of AFNI updates.
Please see 'afni_history -help' for more details.
27 Feb 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed -regress_use_stim_files typo (was -regress_use_stim_times)
26 Feb 2008, RC Reynolds, afni_history, level 1 (MICRO), type 0 (GENERAL)
checked in initial afni_history files
25 Feb 2008, RW Cox, 1dsvd, level 2 (MINOR), type 2 (NEW_OPT)
add '-vmean' and '-vnorm' options, to mirror capabilities in 3dpc
25 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Make 3dTfitter work when -RHS is a '1D:' input (-LHS already worked).
* -vnorm and -vmean options for 1dsvd.c (as in 3dpc.c).
25 Feb 2008, RC Reynolds, plug_vol2surf, level 3 (MAJOR), type 4 (BUG_FIX)
fixed application of cluster for sending data to suma
Previously, clustering was only applied when the Olay and Thr sub-bricks
were the same.
24 Feb 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
GIFTI library now considers MetaData without Value as valid
22 Feb 2008, RW Cox, 3dpc, level 2 (MINOR), type 2 (NEW_OPT)
add '-eigonly' and '-reduce' options; output eigenvalues to a 1D file
'-eigonly' causes 3dpc to print eigenvalues to stdout and stop there.
'-reduce n pp' outputs a reduced dataset, using only the largest 'n'
eigenvalues.
22 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Changes to 3dpc.c: -reduce and -eigonly options.
21 Feb 2008, RC Reynolds, GIFTI, level 4 (SUPER), type 0 (GENERAL)
AFNI programs can now read and write GIFTI datasets
GIFTI datasets are for data in the surface domain, with file suffix .gii.
Support must be requested at compile time, and it requires libexpat.
Please see http://www.nitrc.org/projects/gifti for many details.
20 Feb 2008, RW Cox, 1deval, level 2 (MINOR), type 2 (NEW_OPT)
add '-1D:' option, to write output that is usable on the command line
Sample usage:
1dplot `1deval -1D: -num 71 -expr 'cos(t/2)*exp(-t/19)'`
The backquotes `...` capture command's output and put this string on
the command line. The '-1D:' option formats the 1deval output so that
it is ready to be used in this way.
20 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Add cl2.c constrained least squares function to the library.
* Use this in thd_fitter.c and thence in 3dTfitter.c.
* Add '-1D:' option to 1deval.c.
19 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Bug fixes in 3dTfitter.c and thd_fitter.c.
16 Feb 2008, RW Cox, 3dTfitter, level 4 (SUPER), type 1 (NEW_PROG)
new program = linear fits to voxel time series
Uses L1 or L2 regression, with optional constraints to fit each voxel
time series as a sum of basis time series, which can be 1D files or
3D+time datasets. Basis time series that are 1D time series are
the same for all input voxels. Basis time series that are 3D+time
datasets are different for each voxel.
Differences from 3dDeconvolve:
* Basis time series can vary across voxels.
* Fit coefficients can be found with L1 or L2 error functions, and
can be constrained to be positive or negative.
* 3dTfitter does not compute goodness-of-fit statistics.
16 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* New program 3dTfitter. And fitting function THD_fitter().
14 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Graphing of dset content with 'g'
A graph of the column content at a node can be plotted
This would be the surface equivalent to AFNI's graphing function.
See suma's interactive help 'ctrl+h' for more info.
14 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Similar changes to de-clusterize when a forced view switch occurs when
switching datasets, or when switching datasets to something that
doesn't have data available.
* Also, AFNI_FLASH_VIEWSWITCH to disable Adam Thomas's view switching
flashiness.
13 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modify mcw_glob.c and thd_mastery.c to pre-expand '~/' at the start of
a filename to '${HOME}/' to help some pitiful users (e.g., me).
* Modify afni.c to turn off clusterizing when switching coordinate systems
.
12 Feb 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
An option to show all of suma's environment variables
See help for -environment in suma -help.
11 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Modified afni.c and thd_mastery.c to work better with '3dcalc' command
line datasets.
07 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* DSET_overwrite() macro, and THD_force_ok_overwrite() function.
* Modify plug_drawdset.c to use DSET_overwrite(), and a few other
plugins and 3d*.c programs as well.
* Fix drawing of surface overlay when the functional overlay is being
shown as the underlay: must use the underlay dataset for coordinate
checking even if overlay dataset is actually being drawn as underlay,
since the coordinates for the images are still the underlay's in
this situation.
* Fix 3dvolreg to work properly with sub-brick scale factors.
06 Feb 2008, ZS Saad, SurfDist, level 3 (MAJOR), type 1 (NEW_PROG)
Program to calculate geodesic internodal distances
06 Feb 2008, RC Reynolds, 3dbucket, level 2 (MINOR), type 0 (GENERAL)
modified to copy FDR curves
05 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Fix over-write checks in mri_write.c by moving all file open/close
operations to new fopen_maybe() and fclose_maybe() functions.
* Move THD_deathcon() and THD_ok_overwrite() functions to afni_environ.c,
where they belong.
* New function EDIT_geometry_constructor() to make an empty dataset from
a string specifying it's geometry. Also, print this geometry string
in 3dinfo.
04 Feb 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_NEWSESSION_SWITCH in afni_func.c == switch to new session?
01 Feb 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* VOLUME_DATA_SPARSE in thd_nimlatr.c.
* READ_NIML_FILE in afni_driver.c.
* Force re-clustering when doing a redraw in the ROI plugin.
* Modify NIML+PO button label to reflect status of NIML and plugouts
at time button is created.
31 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify plug_crender.c to obey AFNI_SLAVE_THRTIME.
29 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Fixed bug in 3dFDR -new handling of mask -- ooooppssssie.
* And bug in FDR curves generated from signed statistics (like t).
28 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Added PRINT_COMPILE_DATE macro to mrilib.h and to a lot of programs'
-help output.
* Fixed 'rule of 15' bug in afni_cluster.c, where the initial display only
showed a max of 15 widget rows, even if there were more clusters, but
the number of rows would be reset correctly on any re-clusterizing.
Problem: didn't initialize maxclu_default at the right location.
* Fixed problem with display of clusterized dataset which is both the
Underlay and Overlay: the Underlay was being shown as the edited
volume, but that looks real bad. Solution: disable vedit feature
in AFNI_dataset_slice() when calling from the 'get anat image' place
in afni.c, and then re-enable it right afterwards.
25 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* mri_read_1D_stdin() in mri_read.c.
24 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add FDR curve generation to 3dANOVA.lib, 3dNLfim, 3dRegana, 3dttest.
* Fix little problems with AFNI threshold scale display as q-value alters.
* Fix bug in thd_mastery.c in assiging FDR curves to mastered sub-bricks.
* Add '-killSTAT' option to 3drefit.
23 Jan 2008, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* FDR thresh-vs-z(q) curve generation and storage in datasets.
* Display FDR q in AFNI pval label.
* Generate FDR curves automatically in 3dDeconvolve, and with
'-addFDR' option in 3drefit.
22 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Minor changes to 3dFDR: better help, -float, -qval.
* Add -sort and -SORT options to 3dcalc, for no good reason.
* Add 'help' command to ccalc, to give parser info.
22 Jan 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options to estimate smoothness in data for use in AlphaSim
See help options -regress_est_blur_epits and -regress_est_blur_errts.
18 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 0 (GENERAL)
Older History stuff
* Incorporate mri_fdrize() into 3dFDR.
auto-generated by afni_history on Jul 18 2008