Dear freesurfer, I’m trying to do resting state fMRI analysis in freesurfer. Most of the 1st level analyses look ok, but for few subjects the mas looks strange. Please find an example attached. Could you give me suggestions how to trouble shoot the problem. Thank you! Lauri Tuominen [cid:B7649807-0689-4BEC-A949-1B5D92A4D7C1@partners.org]
That is pretty weird. I would first check the fMRI-FS registration (though I doubt this is the problem). I would then look at the brainmasks. There are several in each fmri run under the masks folder. I would check brain.nii.gz first (using freeview or tkmedit -- does the mask look good? Or does it eat away too much?), then brain.fsaverage.rh.nii.gz (tksurfer loading it as an overlay). Does the left hemi look like this? You can also try analyzing just this subject with -surface self rh when running preproc-sess. I suspect that it might be some issue with the anatomical. Anyway, let me know how these things go.
On 11/09/2016 01:44 PM, Tuominen, Lauri Johannes wrote:
Dear freesurfer, I’m trying to do resting state fMRI analysis in freesurfer. Most of the 1st level analyses look ok, but for few subjects the mas looks strange. Please find an example attached. Could you give me suggestions how to trouble shoot the problem. Thank you! Lauri Tuominen
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Tuominen, Lauri Johannes