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) ----
23 Jul 2008, RC Reynolds, 3dttest, level 2 (MINOR), type 2 (NEW_OPT)
added -base1_dset option, where -base1 value can vary over voxels
Added for M Beauchamp.
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, 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, 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.
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
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.
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
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
11 Jun 2008, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 5 (MODIFY)
Obliquity handling in alignment, more grid options
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
29 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 5 (MODIFY)
allowed for -polort -1 and for sub-brick selection with dataset names
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, 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.
20 May 2008, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
Clusterize: '-' as the filename means write to stdout.
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
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
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, 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, 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
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.
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, 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, 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.
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.
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, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -copy_gifti_meta and -copy_DA_meta options
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
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, DR Glen, python, level 2 (MINOR), type 4 (BUG_FIX)
repaired support for dry_run mode in python scripts
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, 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.
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, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if 1 volume, GERT_Reco_dicom does not give (useless) timing to to3d
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.
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.
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, 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, RC Reynolds, website, level 2 (MINOR), type 5 (MODIFY)
updated the AFNI History website pages, with a table of entries
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, 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)
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, 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.
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.
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.
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.
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.
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
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?
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.
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.
17 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* AFNI_FLOATIZE environment variable for 3dDeconvolve.c and 3dcalc.c.
* mri_fdrize.c function for FDR-z conversion.
12 Jan 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Scroll lists for I T and B selectors in suma
Right click on pulldown menu titles to get
a scroll list instead. This makes selecting from
a long list of options, or columns, much easier.
Right click on 'I' to the left of suma's Intensity Selection
button for an illustration.
09 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* SIGQUIT delay in afni.c, for Jerzy.
28 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Popup menu in clusterize report to set histogram range.
28 Dec 2007, RC Reynolds, gifti_tool, level 3 (MAJOR), type 1 (NEW_PROG)
program to read and write GIFTI datasets
27 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Upgrades to clusterize reporting window: histograms, from/to indexes
on auxiliary dataset, 3dclust and save table buttons, &c.
* Fixed bug in DG's obliquity reporting function in thd_coords.c -- it
didn't check if the input dataset was valid -- caused AFNI to crash.
20 Dec 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* Clusterize reporting window.
19 Dec 2007, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
Use of '[i]' to select node index from surface dset
Square bracket '[]' selection works for surface-based
datasets much like it does for volume-based ones.
In addition, one can use '[i]' to select the indices
of nodes for which data are defined in a particular
surface-based dataset.
For more information, see 'SUMA dataset input options:'
section in the output of ConvertDset -help .
18 Dec 2007, ZS Saad, ROIgrow, level 2 (MINOR), type 1 (NEW_PROG)
Grows regions separately, depending on labels
18 Dec 2007, ZS Saad, ROI2dataset, level 2 (MINOR), type 0 (GENERAL)
Output full datasets if needed
17 Dec 2007, ZS Saad, ConvertDset, level 2 (MINOR), type 0 (GENERAL)
Output of full dsets if needed
This can be used to force a dataset with data
defined on a few nodes to be written out with a
complete list of nodes, using 0 where no data are defined.
06 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add -jpg and -png options to 1dplot.c.
* Add thick line drawing to mri_coxplot.c (by repeated thin line drawing).
03 Dec 2007, RC Reynolds, GIFTI, level 3 (MAJOR), type 0 (GENERAL)
initial release of gifti I/O C API
23 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 1 (NEW_PROG)
Older History stuff
* Modify NI_decode_one_string() in niml_elemio.c to auto-expand buffer
size if string is too long. For festering Lebanese programmers.
* Similarly, modify scan_for_angles() if element header is bigger than
buffer size.
* 'Histogram: Multi' (plug_histog_multi.c) plugin, for Kyle, Alex, & Pat.
20 Nov 2007, RW Cox, 3dTsort, level 3 (MAJOR), type 1 (NEW_PROG)
new program = sorts voxel data along the time axis
This might be useful for sorting the -stim_time_IM beta weights
output be 3dDeconvolve. Perhaps for something else, too?
20 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 1 (NEW_PROG)
Older History stuff
* Copy auxdata from source to output in 3dAllineate.c (oops).
* Changed 'report' from mri_clusterize.c and added info to the
clusterize vector chooser using about BHelp to see this report.
* New program 3dTsort.c. Will this grow to be a monster?
19 Nov 2007, ZS Saad, Surf2VolCoord, level 2 (MINOR), type 1 (NEW_PROG)
Program to show surface-node to voxel correspondence
This can be used to understand how surface coordinates
relate to voxel coordinates.
16 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Added -global_times, -local_times, and -guess_times to 3dDeconvolve.c
* For ragged 1D input files, arbitrary text starting with alphabetic
character is same as '*' for filler.
* AFNI_RESCAN_AT_SWITCH is on by default now.
* 1dplot takes a 1 row file and flips it to a column for plotting; however
,
when 2 single row files were input, they'd be catenated and THEN
flipped, producing erroneous joined plot. Now, they are flipped
THEN catenated, which does the right thing.
* Speaking of 1dplot, '-nopush' now works for multiple graphs, rather
than just for '-one'.
* Modify AlphaSim.c so that rmm defaults to -1 ==> nearest neighbors,
and so that '-seed 0' generates a custom seed.
* Add some extra text to the 'Clusterize' label (afni_setup.c) to
explain that rmm=0 means NN clustering with vmul in voxel count.
15 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to interactive AFNI to save '1D:' ref and ort files in the
header of interactive fim files; example
1dplot '`3dAttribute -ssep ' ' AFNI_FIM_REF r1_time@1+orig`'
* Changes to mri_read_1D() to allow arbitrarily long filenames.
* New function mri_to1Dstring(), to create '1D:' strings from MRI_IMAGEs.
12 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Changes to bbox.c to add an arrowval index selector to the single-select
ion
mode strlist chooser (per Shruti Japee's unreasonable demand).
11 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify edt_filtervol.c to clip off voxels outside the fmask.
* Modify 3dmerge.c to add -1fm_noclip and -1filter_blur options.
10 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to 3dDeconvolve.c to check -stim_label values: for un-assigned
values, and for duplicate values.
* Change a few programs to check EQUIV_GRIDS() as well as voxel counts,
when combining multiple datasets (3dTcat, etc).
* Modify plug_nth_dataset.c to use different set of default overlay colors
.
Modify afni_plugin.[ch] to allow this.
* Modify afni_graph.c to make 'Transform 1D' menu re-activate a button eve
n
if it is already the activated one. Goal: popup Dataset#N plugin
controls more easily.
* Modify 3dttest.c to add the -sdn1 option (for Tom Johnstone).
04 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify afni_graph.c to turn Double Plot on when Dataset#N is invoked,
and to not double plot transformed time series that didn't change.
* Print 'NFirst > 0' informational message in 3dDeconvolve.c.
* Change OPACITY_BOT from 0 to 1 in imseq.c.
26 Sep 2007, ZS Saad, SurfFWHM, level 4 (SUPER), type 1 (NEW_PROG)
Program to estimate FWHM of data on surface
26 Sep 2007, ZS Saad, SurfSmooth, level 3 (MAJOR), type 5 (MODIFY)
Big changes to data smoothing functions
* HEAT_07 method does controlled blurring, with options
to blur 'to' a particular FWHM. No guessing needed for
iterative kernel bandwidth or number of iterations.
* HEAT_05 method improved to reduce numerical precision
problems.
20 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add '-allcost' options to 3dAllineate.c and mri_genalign.c.
* Neuter program 3dAcost.c.
* Environment variable AFNI_INDEX_SCROLLREV.
20 Sep 2007, G Chen, 3dLME.R, level 4 (SUPER), type 1 (NEW_PROG)
An R program that runs linear mixed-effects analysis at group level in AFNI.
See more details on: http://afni.nimh.nih.gov/sscc/gangc/lme.html
18 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'RGB:r,g,b' format to DC_parse_color() in display.c.
* Fixed some bugs in 'Clipped' display.
17 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'Clipped' option to image grayscaling, in imseq.c and afni.c.
12 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'All AFNI Splashes' button to 'hidden' menu, just for fun.
10 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Minor changes to 3dAllineate.c: '-autoweight**1.5' sub-option;
'-autoweight' now the default for '-ls' cost function.
* Re-insert older fixes to afni.c that were lost in CVS.
31 Aug 2007, RC Reynolds, DECONFLICT, level 3 (MAJOR), type 5 (MODIFY)
modified default behavior of programs from deconflict to no overwrite
See AFNI_DECONFLICT in README.environment.
31 Aug 2007, RC Reynolds, model_conv_diffgamma, level 2 (MINOR), type 1 (NEW_PROG)
NLfim model to compute the convolution of the difference of gammas
20 Aug 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* First version of '-lpc' Local Pearson Correlation cost function in
3dAllineate.c, with rhombic dodecahedra as the default building bloks.
14 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify 3dDeconvolve.c to allow 'POLY' model to have order up to 20.
* Modify 3dLocalBistat.c to allow '-weight' option for '-pearson' statisti
c.
08 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add threshold signage feature to AFNI threshold menu ('Pos & Neg', etc).
03 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_SEE_OVERLAY environment variable.
* Turn overlay on when user first-time switches Overlay, and turn TTatlas
colors on when user pops up atlas color chooser panel.
31 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Make -cmass the default in 3dAllineate.c.
* Also add '+clip' feature to '-autoweight' in 3dAllineate.c.
30 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify thd_read_vecmat.c to use mri_read_double_ascii() to read a file r
ather
than read it directly. This way, comments will be skipped properly and
the '1D: ...' format can be used.
* Fix afni_plugin.c to initialize loading of matrix_initialize(), to fix a
problem left in plug_deconvolve.c by RCR's matrix.c changes.
* Matrix square root in mri_matrix.c, and thence to 1dmatcalc and cat_matv
ec.
30 Jul 2007, RC Reynolds, regression_tests, level 3 (MAJOR), type 0 (GENERAL)
added setup for regression testing to NIFTI package
This can be used as a template for testing any command-line programs.
27 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add 'SPMG3' to 3dDeconvolve.c.
* Fix bug in -1Dmatrix_save in 3dAllineate, when dealing with zero-padded
base.
25 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dAllineate, 3dvolreg, and 3dWarpDrive to output base-to-source m
atrices.
* Modify cat_matvec to deal with files of multiple matrices.
* Modify 3dAllineate to make '-clbin 0' the default.
* Modify afni to add an AutoThreshold button to the threshold popup menu.
16 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -stim_times_IM to 3dDeconvolve.c, to get individual event amplitudes
.
29 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Boxed plots work with Dataset#N now, in glorious colors and thinned.
But not with Double Plot.
28 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Threshold on/off in reactivated thr_label popup menu in Define Overlay.
* -x1D_stop in 3dDeconvolve.
26 Jun 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* Boxed plots in afni_graph.[ch]. Probably a can of worms.
25 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to 3dDeconvolve and 3dSynthesize so that censored time points
can be reconstructed in some fashion in the latter program.
* -x1D_uncensored in 3dDeconvolve.
06 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify thd_writedset.c to always do THD_deconflict_prefix(), unless told
not to by AFNI_DONT_DECONFLICT. Modify a bunch of 3d programs to NOT
check for filename conflict on output.
* Modify thd_correlate.c build_2Dhist() to avoid histogram overflow (oops)
.
05 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dBlurToFWHM.c and 3dFWHMx.c to use detrending.
* Add THD_patch_dxyz_* functions to thd_auxdata.c, to make sure MRI_IMAGE'
s
in a dataset have the correct dx,dy,dz fields.
30 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dDeconvolve mmap() usage to include MAP_NORESERVE flag.
* Add -allzero_OK option to 3dDeconvolve.c.
* Make 3dttest check for duplicate dataset filenames.
09 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New advanced histogram options '-clbin' and '-eqbin' for 3dAllineate.
04 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* 'amongst' function in parser.f and so in 3dcalc.c.
* Added more warnings to 3dDeconvolve.c, including a parametrized -GOFORIT
.
03 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'crop=' to afni_driver.c image window opening, and also to afni_sp
lash.c
when saving .afni.startup_script file. [Per John Butman]
* Modified 3dDeconvolve.c to print clearer messages when -gltsym errors
occur, and also to allow the Decon -bucket dataset to be overwritten,
and also to add the -nobucket option. [Per Mike Beauchamp]
30 Apr 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Included 3dinfo.c patch from Colm Connolly with -label2index option.
26 Apr 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify imseq.[ch], afni.c, and afni_graph.c to use '[' and ']' keys for
time index incrementing, per John Butman.
04 Apr 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dDespike.c to add -localedit option.
* Modify 3dAllineate.c to save matrices into header of output.
26 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Moved on-the-fly cluster editing to Define Overlay panel, from popup men
u.
23 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New function THD_deconflict_prefix() in thd_opendset.c.
* Modify 3dDeconvolve.c to deconflict output prefixes (instead of failing)
,
and to compute Full F by default, unless -nofullf_atall is given.
* AFNI_IMAGRA_CLOSER, for the FC5 abusers out there.
21 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New program 3dEmpty.c.
* Fix 3dinfo.c to allow empty datasets (duh).
16 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* -polort A and polort degree warning message.
* Change CTENT() to CSPLIN().
15 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added CTENT() to 3dDeconvolve.c, for experimental purposes.
* Modified bucket labels in 3dDeconvolve.c to be clearer (to me, anyhoo).
14 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New program 1dMarry.c.
13 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Minor changes to 3dSynthesize.
* Change PRINT_VERSION() macro in mrilib.h to include compilation __DATE__
in output.
* '-float' option to 3dDeconvolve. Also a few little other fixes.
12 Mar 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* New program 3dSynthesize.c.
10 Mar 2007, ZS Saad, MapIcosahedron, level 2 (MINOR), type 5 (MODIFY)
Better handling of surface centers
09 Mar 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* First test of -stim_times_AM? looks good.
* MCW_discard_events() for Button4/5 ScrollWheel actions.
07 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* 3dDeconvolve.c: -GOFORIT, check_matrix_condition(), report -stim_times
values outside of run intervals, condition numbers with and without
baseline regressors.
05 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -nfft and -detrend options to 3dDFT.
* Added 'u' and 'o' image viewer keypress handling to afni.c.
* Added Mod+Button4+5 threshold slider changing to imseq.c and afni.c.
* Added AFNI_THRESH_AUTO to afni_func.c.
01 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add dilation to -automask option in 3dAllineate. And -ignout option.
* Add -CENSOR to 3dDeconvolve.c.
27 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_DISABLE_TEAROFF environment variable.
21 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified Edit Environment pseudo-plugin (afni_pplug_env.c) to sort
controls by variable name.
* Added 'instant switch on selection' mode to 'Overlay' and 'Underlay'
dataset choosers, controlled by AFNI_DATASET_BROWSE variable.
* And to 'Talairach To' controls.
* Fixed bug when '-R' would fail to find any datasets, and would then
try to reconcile parents, look for duplicates, etc., de-referencing
NULL pointers. Not sure what happened, actually, but one technique
was to avoid trying to read directories as regular file datasets.
18 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* When running 'afni' (no directory args) and no data is found is './',
then afni.c will now recurse 1 level on './' to see if any datasets
can be found 1 level deeper. Inspired by Korea workshop and Hame Park.
15 Feb 2007, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
High resolution image saving with ctrl+r
Very high resolution images can be created.
See suma's interactive help 'ctrl+h' for more info.
05 Feb 2007, ZS Saad, SurfDsetInfo, level 2 (MINOR), type 1 (NEW_PROG)
Program to display surface dataset information
Output is crude at the moment.
02 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added a 'Rescan' button next to 'Overlay' and 'Underlay' in the main
AFNI controller. At the demand of Ziad Saad.
* Later: and a 'NIML+PO' button below that.
17 Jan 2007, G Chen, 1dSEM, level 4 (SUPER), type 1 (NEW_PROG)
An AFNI program that runs path analysis (or structural equation modeling) at
group level.
See more details on: http://afni.nimh.nih.gov/sscc/gangc/PathAna.html
15 Jan 2007, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Allow replacement of pre-loaded DO and Dsets
When a dataset is reloaded, it replaces the one
already loaded in suma.
05 Jan 2007, ZS Saad, imcat, level 2 (MINOR), type 1 (NEW_PROG)
Program to stitch images.
20 Dec 2006, RC Reynolds, afni_proc.py, level 4 (SUPER), type 1 (NEW_PROG)
program to write complete single subject FMRI processing script
14 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added SAVE_FILTERED to the roster of AFNI driver commands.
11 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* More changes to 3dBlurToFWHM.c -- de-median and de-MAD before blurring a
nd
before estimating blur, to be somewhat more self-consistent.
* Added SAVE_PNG to the roster of AFNI driver commands.
11 Dec 2006, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 1 (NEW_PROG)
program to convert stim_files to stim_times files
08 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -dem option to 1ddot.c.
07 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added movie saving commands to afni_driver.c.
* Modified 3dFWHMx.c -geom option to add up logs rather than multiply up
results -- for large numbers of sub-bricks, can get overflow the old wa
y.
* Added THD_medmad_bricks() and THD_meansigma_bricks() functions to
thd_median.c -- get location and dispersion statistics at same time,
for speed.
30 Nov 2006, ZS Saad, suma, level 2 (MINOR), type 0 (GENERAL)
Addition of new Displayable Objects (DO)(ctrl+Alt+s)
Allows display of segments, spheres and other markers
See suma's interactive help 'ctrl+h' for more info.
20 Nov 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Multitudinous changes to 3dBlurToFWHM.c.
15 Nov 2006, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* New program 3dBlurToFWHM.c.
09 Nov 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dFWHM to do what 3dFWHMx does -- not use a voxel in a differen
ce
unless it is in the mask as well.
31 Oct 2006, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* New program 3dFWHMx -- does all sub-bricks.
30 Oct 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified plug_scatplot.c to copy 'Aboot' option from plug_histog.c.
* Modified THD_pearson() stuff in thd_correlate.c to remove mean.
* New program 3dLocalBistat.c -- joint local statistics between 2
datasets.
24 Oct 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dAutomask.c (etc.) to add -peel and -nbhr options, with
also a fix to stupid error made a couple days before.
22 Oct 2006, RC Reynolds, model_demri_3, level 3 (MAJOR), type 1 (NEW_PROG)
NLfim model for Dynamic Enhanced MRI
12 Oct 2006, RC Reynolds, serial_writer, level 2 (MINOR), type 1 (NEW_PROG)
program to send data from a file, pipe or made up to a given serial port
10 Oct 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dClipLevel.c to allow float input datasets.
* Modified 3drefit.c to make '-TR' option add a timeaxis to a non-3D+time
dataset.
* More changes to 3dAllineate.c.
* Program 3dAcost.c to compute 3dAllineate costs on 2 bricks [now gone].
29 Sep 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* 3dAllineate.c edited to make -linear the default interpolation during
alignment process, and -cubic for the output dataset.
27 Sep 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified correlation ratio in thd_correlate.c to use both Var(y|x) and
Var(x|y) for symmetry between base and target. Seems to make
registration work better.
* Added -check and -master options to 3dAllineate.c.
21 Sep 2006, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* Put 3dAllineate into the distribution. But is not finished.
* Modified plug_nlfit.c to allow AFNI_NLFIM_METHOD to select optimizer.
20 Sep 2006, ZS Saad, DriveSuma, level 3 (MAJOR), type 1 (NEW_PROG)
Program to control SUMA from the command line
05 Sep 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Mod mri_read_1D() so that ending filename in ' character causes
transposition. Removed this feature from thd_1Ddset.c to match.
* Changes to AFNI to allow on-the-fly cluster editing.
14 Aug 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add pairmax() to parser.f.
08 Aug 2006, RC Reynolds, C++, level 2 (MINOR), type 5 (MODIFY)
afni program compiles in C++ (effort with Rich and Greg Balls)
04 Aug 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add max displacement to 3dvolreg.c.
03 Aug 2006, RC Reynolds, NI_SURF_DSET, level 4 (SUPER), type 0 (GENERAL)
added a new surface dataset format, with read/write ability in AFNI
auto-generated by afni_history on Jul 24 2008