Dear FS experts,
I would like to strip skulls from unregistered images which have gone through GradWarp, B1-correction, N3 normalization and phantom-based scaling. I run the following two commands in freeSurfer: recon-all -autorecon1 -subjid <subjid> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
My questions are
1) Currently I use 5 as threshold (-T 5). Is there a guidance for the setting of this parameter?
2) In the output file T1.final.mgz, is the skull-stripped image represented in ijk space (image index space) or in XYZ space (via transformation matrix)?
3) If the skull-stripped image is represented in XYZ space, how do I get it in ijk space?
Thanks in advance for the help!
Best Regards, Yi Li (PhD) Senior Computational Scientist Computational Sciences The Jackson Laboratory Farmington, CT 06032 Tel: 860-837-2156
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