Work-in-progress : adding subject-specific options in the fMRI preprocessing pipeline.



git-svn-id: http://niak.googlecode.com/svn/trunk@1324 3762db0e-9444-0410-bee5-d3813040ea1c
1. Bug fix in subject-specific preprocessing parameters for the fMRI preprocessing pipeline.
2. The region growing is now turned off by default in the fMRI preprocessing pipeline.


git-svn-id: http://niak.googlecode.com/svn/trunk@1325 3762db0e-9444-0410-bee5-d3813040ea1c
1. Bug fix in the last commit
2. Used the ability to specify different parameters for some of the subjects in NIAK_DEMO_FMRI_PREPROCESS.



git-svn-id: http://niak.googlecode.com/svn/trunk@1326 3762db0e-9444-0410-bee5-d3813040ea1c
A new tool to estimate partial volume effects on T1 volumes, thanks to Jussi Tokha !



git-svn-id: http://niak.googlecode.com/svn/trunk@1327 3762db0e-9444-0410-bee5-d3813040ea1c
Minor bug fixes.



git-svn-id: http://niak.googlecode.com/svn/trunk@1328 3762db0e-9444-0410-bee5-d3813040ea1c
Bug fix.



git-svn-id: http://niak.googlecode.com/svn/trunk@1329 3762db0e-9444-0410-bee5-d3813040ea1c
Forgot a strategic ;



git-svn-id: http://niak.googlecode.com/svn/trunk@1330 3762db0e-9444-0410-bee5-d3813040ea1c
Added estimation of partial volume effects in the fMRI preprocessing pipeline (development version).



git-svn-id: http://niak.googlecode.com/svn/trunk@1331 3762db0e-9444-0410-bee5-d3813040ea1c
1. Added the option for PVE estimation in the master fMRI preprocessing pipeline.
2. Deleted the "dev" version of the fMRI preprocessing pipeline, which is currently deprecated.



git-svn-id: http://niak.googlecode.com/svn/trunk@1332 3762db0e-9444-0410-bee5-d3813040ea1c
Bug fix.



git-svn-id: http://niak.googlecode.com/svn/trunk@1333 3762db0e-9444-0410-bee5-d3813040ea1c
fix bug and add regress confounds capability


git-svn-id: http://niak.googlecode.com/svn/trunk@1334 3762db0e-9444-0410-bee5-d3813040ea1c
Major changes in the NIFTI reader/writer:
1. The reader now reads the quaternion affine transformation, if there is no "sform" transformation.
2. The data is written in double type, always. This is to avoid issues with data types.
3. The data is always written with an "sform" transformation, which is updated based on HDR.INFO.MAT 
   (overrides whatever is in the header).



git-svn-id: http://niak.googlecode.com/svn/trunk@1335 3762db0e-9444-0410-bee5-d3813040ea1c
add command niak_glm you can now do normal regression, t-test and f-test



git-svn-id: http://niak.googlecode.com/svn/trunk@1336 3762db0e-9444-0410-bee5-d3813040ea1c
Add QC for each covar family (f-test)



git-svn-id: http://niak.googlecode.com/svn/trunk@1337 3762db0e-9444-0410-bee5-d3813040ea1c
A new command to average time series associated with atoms on a set of clusters (the atoms are matched with clusters, and the average accounts for differences in size between atoms).



git-svn-id: http://niak.googlecode.com/svn/trunk@1338 3762db0e-9444-0410-bee5-d3813040ea1c
Fix a small bug with pve
add qc var explained for corsica and motion correction




git-svn-id: http://niak.googlecode.com/svn/trunk@1339 3762db0e-9444-0410-bee5-d3813040ea1c
Got rid of a couple of deprecated functions.



git-svn-id: http://niak.googlecode.com/svn/trunk@1340 3762db0e-9444-0410-bee5-d3813040ea1c
fix bugs



git-svn-id: http://niak.googlecode.com/svn/trunk@1341 3762db0e-9444-0410-bee5-d3813040ea1c
Two new commands to work on a so so-called FMRI structure. FMRI usually has three levels of nested fields, generally called <SUBJECT>, <SESSION> and <RUN> (each level actually features an arbitrary number of arbitrary fields). The two commands are designed to re-arrange an fMRI structure:
  1. NIAK_FMRI2STRUCT : takes an FMRI structure where <SESSION> is a cell of strings instead of a structure, and replace it by a structure with default names for runs ('run1', 'run2', etc).
  2. NIAK_FMRI2CELL : extract the values of all runs in a big cell of string. Also builds a LABEL structure to keep track of the values of <SUBJECT>, <SESSION> and <RUN> for each entry.
 


git-svn-id: http://niak.googlecode.com/svn/trunk@1342 3762db0e-9444-0410-bee5-d3813040ea1c
clean code and fix bugs


git-svn-id: http://niak.googlecode.com/svn/trunk@1343 3762db0e-9444-0410-bee5-d3813040ea1c