How Can I Keep up Brain-stem and Cerebellum while Creating .pial and .inflated Surfaces by using "Recon all" Command?
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Dear Freesurfer Experts,
I need a brain cortex surface including Brain-stem and Cerebellum. Using "recon-all" command, Brain-stem and Cerebellum has been removed from the output pial files. How can I set the command in order to keep up Brain-stem and Cerebellum with brain cortex surface?
I would appreciated any help.
Regards,
Mahshid
Hi Mahsid,
you can use mri_mc or mri_tessellate to create a mesh for them using the aseg as input if you want. The cerebellum in particularly will have a seriously incorrect topology as we can't see the majority of the folia at in vivo resolutions.
cheers Bruce
On Sat, 11 May 2019, Mahshid Fouladivanda wrote:
External Email - Use Caution
Dear Freesurfer Experts, I need a brain cortex surface including Brain-stem and Cerebellum. Using "recon-all" command, Brain-stem and Cerebellum has been removed from the output pial files. How can I set the command in order to keep up Brain-stem and Cerebellum with brain cortex surface? I would appreciated any help. Regards, Mahshid
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Mahshid Fouladivanda