Hi Yi
yes, brainmask.mgz is the skull stripped image.
And no, n3 is pretty gentle so I would think letting our normal intensity normalization run would be fine (and better than not doing it)
cheers Bruce
On Mon, 13 Nov 2017, Yi Li wrote:
Hi Bruce,
Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
Another question: since my raw image has gone through B1 correction and N3 normalization, will you suggest I omit the nu and normalize step in -autorecon1?
Best Regards, Yi
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 10:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [strip skull for unregistered images]
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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