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.
