Hi Sampada

you need to identify why you are getting excessive topologic defects. Can you send an image of one of your acquisitions?

Bruce On Tue, 23 Feb 2016, Dr Sampada Sinha wrote:

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