Hi Yi
autorecon1 should do the skull stripping, so there is no need for the
separate mri_mask call. The threshold of '5' is so to preserve edits in
which voxels are turned 'off' (they are set to 1 I believe, but we reserve
2-4 as additional 'off' values).
The masking will not transform the voxel coordinates of the image
cheers
Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
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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