Hello experts,

 I am getting skull strip issues with FreeSurfer recon-all runs in every data.

I ran recon-all on my T1-data and noticed that the skullstrip is not so good. Almost in every subjects there were  dura included, so I tried the suggestion of using the flags -skullstrip and -Clean–bm and –gcut in my recon-all command line for one subject. Forexmaple:

I ran reconall using the following command lin:

recon-all –skullstrip first -clean–bm –gcut –s AA***.T* -all -use–mritotal 

The run was complete and I looked at the brainmask.mgz file of the output. But I didn't see any correction.

I am attaching the jpg image of the sagittal view of brainmask.nii ( I converted the mgz file to nii to view tham in afni)

SubjFS: is the image from recon-all run

SubjFS: is the image  from recon-all that was run with Skullstrip/clean-bm/gcut options included.

Did I do anything wrong?

Your guidance and suggestion needed.

Thanks,

Rashmi.