Sometimes the stroke will mess up the analysis in the undamaged hemi. A lot of times people will make a mask of the stroke area, left-right reverse the brain and register it to itself, then map the contralateral hemi into the voxels of the stroke, then run recon-all on this modified image.

On 11/15/2022 1:01 PM, Huang, Yujing wrote:

Hi Steve,

You can use ‘-hemi <lh|rh>’ to select which hemisphere to process. If you are interested in right hemisphere only, pass ‘-hemi rh’ to recon-all along with other flags.

I don’t have answers to your first question.

Best,

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Steve Petersen *Sent:* Tuesday, November 15, 2022 11:39 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Recon-all in post stroke aphasic patients.

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Dear FreeSurfer experts,

I would like to run the recon-all command in MRI images of post-stroke aphasic patients. Should I use a particular flag in the recon-all command to avoid important errors during cortical reconstruction?. We are only interested in the right hemisphere (where there is no brain injury), can I conduct the recon-all only in the right hemisphere?.

Any help would be appreciated.

Thank you very much in advance.

Best regards,

Steve.

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