i, May 9, 2008 at 8:21 PM
Subject: Re: [Freesurfer] Re: mri_mask
To: Daniel H Choi <[EMAIL PROTECTED]>
Cc: Krish Subramaniam <[EMAIL PROTECTED]>
Hi Daniel,
I just tested this on some data and it seemed to work for me. Can you
run
mri_info on the lh.STG.mgz volume and send us the resul
0. 0. 1.
> >
> >
> > Anil.
> >
> >
> > On Sat, May 10, 2008 at 1:50 PM, Daniel H Choi <
> > [EMAIL PROTECTED]>
> > wrote:
> >
> > Hey Anil,
> > >
> > > This is what Bruce sent me just in case you n
0. 0. 1.
> >
> >
> > Anil.
> >
> >
> > On Sat, May 10, 2008 at 1:50 PM, Daniel H Choi <
> > [EMAIL PROTECTED]>
> > wrote:
> >
> > Hey Anil,
> > >
> > > This is what Bruce sent me just in case you n
Please note the command we used:
mri_mask brainmask.mgz lh.stg.mask.mgz brainout.mgz
and the result we got was:
Writing masked volume to brainout.mgz...done.
On Fri, May 9, 2008 at 2:39 PM, Daniel H Choi <[EMAIL PROTECTED]>
wrote:
> Hi,
>
> I have tried applying a binary mask, specifically for
=
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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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&#
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
Reply | Reply to all
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.
> Hi Bruce,
>
> The exact input is:
>
> mri_mask T1.mgz brain.mgz brain.mgz
>
> This com
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 editin
