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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