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

Kaustubh Patil kaustubh.patil at gmail.com
Sat Dec 19 21:26:36 UTC 2015

Hi Yaroslav,

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

Again, thanks for your help.


PS: this might be a naive question but will help me a lot as I am quite new
to this analysis

On Sat, Dec 19, 2015 at 3:51 PM, Yaroslav Halchenko <debian at onerussian.com>

> On Sat, 19 Dec 2015, Kaustubh Patil wrote:
> > Hi,
> > I want to use PyMVPA for whole-brain searchlight analysis on some
> existing
> > data. The data has been already preprocessed (skull stripping, motion
> > correction etc.). Each subject data contains 10 runs and each run was
> processed
> > separately, so there is a separate full brain boolean mask for each run.
> > My question is what is the recommended/correct a way to use this data to
> > perform run-wise cross-validation searchlight?
> you have a problem here, since you have done per run preprocessing, in
> particular motion-correction, your volumes are misaligned across runs.
> (used FSL, didn't you? )
> ideally, you redo preprocessing while motion correcting to the same
> volume across all the runs.  Alternatively, you reslice all the runs
> into the same space (could well be the common space your toolkit used
> for analysis across runs -- common anatomical or MNI) and then do
> analysis there, while again unifying your mask, which must be the same
> across all the runs.
> > As I understand, each run has to be in the same space (same number of
> voxels)
> > so that training and test can be performed, so the whole brain masks
> have to be
> > somehow aligned. How would you recommend doing this?
> it is not a mere 'number of voxels' problem but rather that you have
> misaligned across runs volumes.  if just voxel number -- choose
> intersection of all masks.
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience     http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
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