Minor bug fix for parameter specification of the REGRESS_CONFOUNDS brick.



git-svn-id: http://niak.googlecode.com/svn/trunk@1383 3762db0e-9444-0410-bee5-d3813040ea1c
Fix the doc for regress confounds


git-svn-id: http://niak.googlecode.com/svn/trunk@1384 3762db0e-9444-0410-bee5-d3813040ea1c
Minor bug fix.



git-svn-id: http://niak.googlecode.com/svn/trunk@1385 3762db0e-9444-0410-bee5-d3813040ea1c
fix a the default for regress confounds


git-svn-id: http://niak.googlecode.com/svn/trunk@1386 3762db0e-9444-0410-bee5-d3813040ea1c
Minor fix for default options in the fMRI preprocessing pipeline.



git-svn-id: http://niak.googlecode.com/svn/trunk@1387 3762db0e-9444-0410-bee5-d3813040ea1c
The QC of both motion correction and CORSICA are now the ratio of variance after/before correction (if one of the variance is zero, ratio is defined as 1). Before it was using energy (sum of squares) rather than variance (sum of squares after correction to zero temporal mean).



git-svn-id: http://niak.googlecode.com/svn/trunk@1388 3762db0e-9444-0410-bee5-d3813040ea1c
Changed the default resampling scheme for 3D volumes from 'tricubic' to 'trilinear'. At low resolution, the tricubic scheme exhibited numerical instabilities.



git-svn-id: http://niak.googlecode.com/svn/trunk@1389 3762db0e-9444-0410-bee5-d3813040ea1c
Bug fix in the interpolation scheme used by QC. 



git-svn-id: http://niak.googlecode.com/svn/trunk@1390 3762db0e-9444-0410-bee5-d3813040ea1c
Added an option to "scrub" time frames with excessive motion, following the method described in Power el al., Neuroimage 2012. There is also a group summary for QC (# of scrubbed frames, # of remaining frames, average FD, average DVARS). This new feature hasn't been tested yet.



git-svn-id: http://niak.googlecode.com/svn/trunk@1391 3762db0e-9444-0410-bee5-d3813040ea1c
Bug fixes in the last commit.



git-svn-id: http://niak.googlecode.com/svn/trunk@1392 3762db0e-9444-0410-bee5-d3813040ea1c
Another bug fix in the recent update.



git-svn-id: http://niak.googlecode.com/svn/trunk@1393 3762db0e-9444-0410-bee5-d3813040ea1c
Oooops made a (kind of a) mistake in the implementation of the "scrubbing" method. The scrubbing was done prior to multiple regression of global average etc ... This inflated the values of DVARS and rendered the threshold proposed in Power et al. 2012 irrelevant. It's now done after. More tests to come ...



git-svn-id: http://niak.googlecode.com/svn/trunk@1394 3762db0e-9444-0410-bee5-d3813040ea1c
A number of bug fixes.



git-svn-id: http://niak.googlecode.com/svn/trunk@1395 3762db0e-9444-0410-bee5-d3813040ea1c
Got rid of DVARS in the scrubbing of time frames with excessive motion. The selection is now purely based on FD.



git-svn-id: http://niak.googlecode.com/svn/trunk@1396 3762db0e-9444-0410-bee5-d3813040ea1c
Yet another bug fix. The scrubbing procedure should be good to go now.



git-svn-id: http://niak.googlecode.com/svn/trunk@1397 3762db0e-9444-0410-bee5-d3813040ea1c
Minor modifs:

1. Added an option in NIAK_BRICK_QC_SCRUBBING to set the threshold on acceptable FD.
2. Changed the name of the output of NIAK_BRICK_QC_SCRUBBING.



git-svn-id: http://niak.googlecode.com/svn/trunk@1398 3762db0e-9444-0410-bee5-d3813040ea1c
Added a flag to keep the results of the motion correction.



git-svn-id: http://niak.googlecode.com/svn/trunk@1399 3762db0e-9444-0410-bee5-d3813040ea1c
One more change in the "scrubbing" method to be closer of the algorithm published by Power et al. When a time frame has a FD above the acceptable threshold, the frame before and the two frames after are discarded as well. 



git-svn-id: http://niak.googlecode.com/svn/trunk@1400 3762db0e-9444-0410-bee5-d3813040ea1c
add stf_eff to results output



git-svn-id: http://niak.googlecode.com/svn/trunk@1401 3762db0e-9444-0410-bee5-d3813040ea1c
Bug fix in the default smoothing parameters.



git-svn-id: http://niak.googlecode.com/svn/trunk@1402 3762db0e-9444-0410-bee5-d3813040ea1c