Hi Doug,
For mri_mask's threshold,
"mri_mask -T 1 T1.mgz brain.mgz brain.mgz" works, but
"mri_mask -T 0 T1.mgz brain.mgz brain.mgz" does not work, and
"mri_mask T1.mgz brain.mgz brain.mgz" does not work either.
So one should specify the threshold to be at least 1. The default used by
-autorecon2 (or normalization2) is not sufficient.
--Yuhong
=============================================================================
Yuhong Jiang [EMAIL PROTECTED]
617-876-2054 http://web.mit.edu/yuhong/www
=============================================================================
From: [EMAIL PROTECTED] <[EMAIL PROTECTED]>
To: Yuhong Jiang <[EMAIL PROTECTED]>
Cc: freesurfer@nmr.mgh.harvard.edu, [EMAIL PROTECTED]
Date: Jan 7, 2006 2:43 PM
Subject: Re: [Freesurfer] Re: mri_mask bug
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garbled?
it sounds like there's something that went wrong with the skullstripping
if you have to use a threshold of 20. Have you looked at brain.mgz
immediately after skullstripping? The background voxels should be 0.
On Fri, 6 Jan 2006, Yuhong Jiang wrote:
Hi Bruce,
The exact input is:
mri_mask T1.mgz brain.mgz brain.mgz
This command was invoked by "recon-all -subjid subject
-normalization2", which is part of "recon-all -subjid subject
-autorecon2". Because of the bug, after this command, the manual
edited brain.mgz went back to pre-manual editing state.
It appears that by adding a threshold (mri_mask -T 20 T1.mgz brain.mgz
brain.mgz) the mask is properly executed. However, this does mean that
one cannot run autorecon2 or normalization2, which calls for mri_mask
without specifying a threshold. Perhaps someone should fix this
command (as well as autorecon2 and normalization2)??
--Yuhong
=============================================================================
Yuhong Jiang [EMAIL PROTECTED]
617-876-2054 http://web.mit.edu/yuhong/www
=============================================================================
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