Re: [Freesurfer] ROIs in midline for cortical thickness

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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