Re: [Freesurfer] Gray matter mask
You have to run recon-all through to the end. You can then extract a GM mask from that. You will need to register your PET image to the anatomical (mri_coreg), map the PET into the anatomical space, then use mri_segstats to compute the mean PET in the GM mask. Alternatively, you may want to use PETsurfer (search for it on the wiki). On 2/6/18 11:06 AM, Hanna Vasilevskaya wrote: Hello FS team, I am new to FS and using version 5.3 on a Mac. I have minimal programming background and this might be a very easy question, however I was not able to find a similar one in the archive. I have T1 MRI images from multiple subjects and I need to extract the brain gray matter mask (just cortical regions, without cerebellum). I will then use this mask as an ROI to extract PET activity. Would you happen to know a way for this? Thank you greatly, Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Gray Matter Mask - twist on previous post
Hi Emily, is it a volume or surface functional map? If volume, I think it should be pretty straightforward to sample it onto the surface with mri_vol2surf then go from there. There is probably a way to do this in SUMA also. cheers, Bruce On Wed, 9 Jan 2008, Emily Trittschuh wrote: Dear Group, Back in April, Anil Roy posted a question about methods to generate a gray matter mask that can be fed into AFNI . . . I'm wondering if the opposite can be done? Can a functional mask made in AFNI be fed easily into Freesurfer? Currently this mask is saved as a NIFTI dataset. Thank you. Emily Emily Trittschuh, PhD Neuropsychology Post-doctoral Fellow Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11-579 Chicago, IL 60611 phone 312/503-1155 fax 312/908-8789 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Gray matter mask
Do you mean cortical masks? If so, then {lh,rh}.ribbon.mgz are binary
masks. You can convert them to nifti with:
mri_convert lh.ribbon.mgz lh.ribbon.nii
doug
Anil Roy wrote:
Hello all,
Is there a method to generate a gray matter mask in Freesurfer that
can be fed into AFNI. Could you please point me to any existing
documentation on the FS wiki that already does this as I was unable to
find anything.
Thanks a lot,
Anil.
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