I see. Have you run recon-all on each hemi? If so, use bbregister to register the surfaces to the fmri data, then use mri_vol2surf to map the activations on to the left and right surfaces and draw your ROIs that way.

cheers

Bruce
On Wed, 1 Feb 2017, Sahil Bajaj wrote:

Hi Dr. Fischl,
Thank you so much for your reply.

I have this SMA activation from a fMRI task. I am interested in getting
cortical thickness of exactly the same area. Its showing activation in both
hemispheres. I am also attaching here screen shot to make it more clear how
it looks like. To do that, thats correct, I am trying to draw both left and
right SMA thickness.

Thanks.

On Wed, Feb 1, 2017 at 2:46 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Sahil

      can you clarify what you mean. Do you have the left hemi SMA
      labeled in MNI space and it (incorrectly) extends into the right
      hemi? Or are you trying to draw both the left and the right SMA?

      Bruce
      On Wed, 1 Feb 2017, Sahil Bajaj wrote:

            Hi everyone,
            I have supplementary motor area (SMA) defined in
            standard MNI volume space
            and I would like to extract cortical thickness for
            this area. I have 80% of
            SMA in left hemisphere and 20% on right hemisphere.
            So I am stuck at the
            command mri_vol2surf before proceeding to
            mri_segstats.

            In mri_vol2surf, I am not sure what should I specify
            for --hemi i.e. whether
            its left or right hemisphere (lh or rh). If I
            specify e.g. lh, then would
            not it convert left hemisphere SMA voxels to surface
            and later on extract
            the measure from left hemisphere only and vice-versa
            for right hemisphere.

            I am not sure how would that work if portion of ROI
            is on both hemispheres
            and how can I run mri_vol2surf command? 

            Thanks,
            Sahil


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