visualizer for correlation matrix (the output are the mean and std of the group + a video of individual matrix)


git-svn-id: http://niak.googlecode.com/svn/trunk@1422 3762db0e-9444-0410-bee5-d3813040ea1c
Tweaking of the white matter mask for regressing out confounds: excluding voxels from the AAL template (which provide a loose segmentation of the grey matter, including subcortical structures).



git-svn-id: http://niak.googlecode.com/svn/trunk@1423 3762db0e-9444-0410-bee5-d3813040ea1c
Added new steps in the construction of the white matter mask : intersection with the mask of the brain derived from BOLD, and extraction of the largest connex component. 



git-svn-id: http://niak.googlecode.com/svn/trunk@1424 3762db0e-9444-0410-bee5-d3813040ea1c
Minor documentation improvement.



git-svn-id: http://niak.googlecode.com/svn/trunk@1425 3762db0e-9444-0410-bee5-d3813040ea1c
Bug fix in the options of the motion correction.



git-svn-id: http://niak.googlecode.com/svn/trunk@1427 3762db0e-9444-0410-bee5-d3813040ea1c
Added an option in the slice timing to correct for systematic (multiplicative) level difference between odd and even slices. 



git-svn-id: http://niak.googlecode.com/svn/trunk@1428 3762db0e-9444-0410-bee5-d3813040ea1c
1. Added an erosion in the construction of the white matter mask for regressing confounds. 
2. Got rid of a deprecated function.
3. Minor improvements in the documentation.



git-svn-id: http://niak.googlecode.com/svn/trunk@1429 3762db0e-9444-0410-bee5-d3813040ea1c
Erosion of the mask after the detection of the largest connected component for the white matter mask ...



git-svn-id: http://niak.googlecode.com/svn/trunk@1430 3762db0e-9444-0410-bee5-d3813040ea1c
A new mask of pure white matter in stereotaxic space (MNI 2009c) at low resolution (3mm). This will be used to extract the WM signal in functional images to regress it as a confound, after intersection with the individual white matter segmentation (this last set of modifs still have to be implemented in NIAK_BRICK_MASK_CORSICA).



git-svn-id: http://niak.googlecode.com/svn/trunk@1431 3762db0e-9444-0410-bee5-d3813040ea1c
Changed the strategy to generate the individual white matter mask for regressing out the white matter average: it is now an intersection between a pure white matter template and the results of the individual segmentation of the T1 image. 



git-svn-id: http://niak.googlecode.com/svn/trunk@1432 3762db0e-9444-0410-bee5-d3813040ea1c
Included the changes in the generation of the white matter mask in the pipeline. All that needs to be tested now. 



git-svn-id: http://niak.googlecode.com/svn/trunk@1433 3762db0e-9444-0410-bee5-d3813040ea1c
Added a new feature in the reader of 3D/4D volume. If the file that is being read is called toto.ext (where ext is .mnc, .nii, .img or any of these + .gz or whatever extension is used for compressed files) the reader will look for toto_extra.mat. If this file exist, it is assumed to be a matlab/octave file, and all the variables it contains are dumped into a field of the header called hdr.extra. This generic mechanism makes it easy to attach custom information to a file which may not be easy to achieve in a consistent way for all data formats supported in NIAK.
 


git-svn-id: http://niak.googlecode.com/svn/trunk@1434 3762db0e-9444-0410-bee5-d3813040ea1c
New feature in the writer of volumes: whenever a field EXTRA is found in the header, all the fields are saved as variables in a .mat file called <BASE FILE_NAME>_extra.mat



git-svn-id: http://niak.googlecode.com/svn/trunk@1435 3762db0e-9444-0410-bee5-d3813040ea1c
A couple of modifs in the slice timing:
1. The list of suppressed volumes as well as the time associated with each frame (which depends on the slice of reference) is now saved as an extra information in the header. To ensure compatibility with both minc and nifti, this is stored in a .mat file called <BASE FILES_OUT>_extra.mat



git-svn-id: http://niak.googlecode.com/svn/trunk@1436 3762db0e-9444-0410-bee5-d3813040ea1c
A few modifs to take into account the new extra information that comes along with a 3D+t fMRI dataset (time_frames and mask_suppressed). 



git-svn-id: http://niak.googlecode.com/svn/trunk@1437 3762db0e-9444-0410-bee5-d3813040ea1c
Minor modif in the resampling brick to include the extra information contained in toto_extra.mat when resampling 3D+t datasets.



git-svn-id: http://niak.googlecode.com/svn/trunk@1438 3762db0e-9444-0410-bee5-d3813040ea1c
the foo_extra.mat files is not going to be a generic mechanism after all, because it would be impossible to determine what information to retain when transforming a file (e.g. when generating an average temporal volume the temporal info becomes irrelevant). Instead it will be only used to store temporal infos like scrubbing, regressions, etc. 



git-svn-id: http://niak.googlecode.com/svn/trunk@1439 3762db0e-9444-0410-bee5-d3813040ea1c
Fixed the detection of the "extra" file for relative path name. There is actually a new command to build the full path name of a file (whether its original form is full or relative). 



git-svn-id: http://niak.googlecode.com/svn/trunk@1440 3762db0e-9444-0410-bee5-d3813040ea1c
1. Added low-pass filtering in NIAK_BRICK_REGRESS_CONFOUNDS.
2. Added QC for the high frequencies that are removed at this stage.
3. Added a mask of the scrubbing, updated time frames as well as the confounds that have been regressed in the "extra" .mat companion to the fMRI dataset. 



git-svn-id: http://niak.googlecode.com/svn/trunk@1441 3762db0e-9444-0410-bee5-d3813040ea1c
A new command to copy an fMRI dataset under a different name, and copy the extra .mat companion if it can be found. 



git-svn-id: http://niak.googlecode.com/svn/trunk@1442 3762db0e-9444-0410-bee5-d3813040ea1c