Hello freesurfer experts,

I am trying to do T1w analysis using freesurfer. The raw images are in dicom format. However, when I view those raw dicom images, some of the brain areas are missing. I just wanted to ask if there is any tool to reconstruct those missing brain areas in the raw images using freesurfer or I need to discard those participants scan altogether?

Also, because the resolution is not good with 1.5T, I have seen that skull stripping is not good with a large chunk of skull tissue coming in the processed images. I tried to adjust the watershed parameters and somehow it worked, but it wasn't satisfactory. I tried to run it through fsl bet and got a good skull strip. However, after running the recon-all followed by auorecon11 no skull strip command the with autorecon2 and autorecon3 I am getting excessive topologic defect. I am attaching the log file with this email for your perusal

Will greatly appreciate if I can be helped regarding these two problems I am presently facing with the analysis.

Thanks and regards,

Sampada

Pre-doctoral student

India