[pymvpa] searchlight for data with different runs with different masks

[Yaroslav Halchenko]

On Sat, 19 Dec 2015, Kaustubh Patil wrote:

> Thanks a lot for your reply.

> The preprocessing was done by someone else and yes FSL was used.

> If I am to do the preprocessing (realignment and motion correction) what would
> you recommend? 

sorry but not sure what particular recommendation I could give you.  The
only thing is to reiterate that you need to motion-correct/align
to the same volume across runs.  There is multiple ways to do it.  You
can as well redo your preprocessing with FSL just specify to use a
specific volume for mcflirt.  If your data was e.g. in openfmri layout I
could recommend/provide nipype workflow to carry out all the
preprocessing (with your parameters)... but otherwise -- don't want to
impose anything.

as for a quick one, once again, you could either just reslice all your
bold data per run into some common space one way (just apply
transformations to common space) or another (rerunning mcflirt but
pointing to some volume you consider the target one, e.g. the
example_func.nii.gz FSL might have prepared for you already)

> As I mentioned before, there are 10 runs per subject, and I
> would like all the volumes (108 in total) to be aligned.

108 doesn't divide by 10 (and would anyways be too few per run) -- so I
guess you meant 108 per each run.

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
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