Dear freesurfer experts,

I am trying to do analysis of T1w images. However, with one participant, try as I might I am not able to get rid of a portion of skull. I tried all the three methods explained very well on freesurfer skullstrip wiki page. But, the portion of skull still remains. I also tried to run the recon-all after fsl bet process, but then I am getting a large topological error and the process get stuck there for days on end, until I don't close the terminal.

I am attaching all the processed images using ws threshold, multistrip, gc strip and finally of talairach_with_skull_2.lta. I will greatly appreciate if this can be sorted by you all.

Also, I would like to bring to your notice of the command error while doing skullstrip with talairach_with_skull_2.lta. The third command IMHO should be (as it works with this one!):

cp talairach_with_skull.lta talairach_with_skull_2.lta

and not,

cp talairach_with_skull_2.lta talairach_with_skull.lta

Thanks and regards,

Sampada Sinha Pre-doctoral student KGMU, Lucknow India