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.
* External Email - Use Caution *
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer