Do you acquire any other scans, like an mprage, in the same session? If so, the easiest thing to do would be to push that through our recon-all pipeline, then register your MPF images to either the mprage or to surfaces using bbregister and you can transfer whatever parcellations/segmentations you like

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Tuesday, January 9, 2024 2:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]FreeSurfer Error

External Email - Use Caution

Dear Freesurfer Developers,

I am a graduate student working on Macromolecular Proton Fraction (MPF) and I need to generate parcellation for it using Freesurfer. I have read several articles that reported successful results with this method. However, I have encountered some errors when I tried to run Freesurfer on my data. Some of the errors are related to transformation at the talairach, and some are related to missing brain mask. I have been struggling with these issues for four days and I have not been able to process any of my data. I have an urgent deadline for my thesis presentation on Friday and I would appreciate your assistance.

I have subscribed to the mailing list but I have not received a confirmation email yet. I have attached a screenshot of my registration and two examples of my T1 MPF images. Could you please test them on your end and let me know what the problem is and how to fix it?

Thank you for your time and support.

Sincerely,