Hi Doug, Yes the FSL group analysis is in MN152 and then I want map that back to each individual's brain that were analyzed and parcellated using FreeSurfer, so I can extract thickness values from my fMRI regions of interest if that is possible.

Thanks! Vina

Douglas N Greve wrote:

So you're group analysis is in MNI152, and you want to map that to fsaverage or back to each individual?

doug

Vina Goghari wrote:

...

Hello all, I have group contrast fMRI activations analzyed by FSL Flame 1 that I want to extract individual thickness data for each subject from data processed by FreeSurfer? Is that possible and if so, how?

Thanks! Vina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Try running reg-feat2anat on your fmri data. This will register the functional data to the subject's structure (which is not useful for this case). But it will also compute the matrix which registers the anatomical and mni152. This will be in featdir/reg/freesurfer/anat2std.register.dat

First, make sure that the registration looks ok:

tkregister2 --mov $FSLDIR/data/standard/avg152T1.nii.gz --reg anat2std.register.dat --surf

Now you can map your mni152-space results into the subject's volume or surface space. Looks like you want surface, so use this:

mri_vol2surf --mov your152results.nii --reg anat2std.register.dat --hemi lh --projfrac 0.5 --o lh.your152results.mgh

doug

Vina Goghari wrote:

Hi, I did not receive a response to this yet. Does it mean it is not possible?

Thanks!!

Vina Goghari wrote:

...

Hi Doug, Yes the FSL group analysis is in MN152 and then I want map that back to each individual's brain that were analyzed and parcellated using FreeSurfer, so I can extract thickness values from my fMRI regions of interest if that is possible.

Thanks! Vina

Douglas N Greve wrote:

...

So you're group analysis is in MNI152, and you want to map that to fsaverage or back to each individual?

doug

Vina Goghari wrote:

...

Hello all, I have group contrast fMRI activations analzyed by FSL Flame 1 that I want to extract individual thickness data for each subject from data processed by FreeSurfer? Is that possible and if so, how?

Thanks! Vina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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