what version of FS do you have? You can try runing it with -pial pial but
I wouldn't think that is needed. Is the lh.pial in
/misc/data41/yuex/recon_test/test_DB48/surf/
and is it readable?
On Wed, 10 Dec 2014, Xiaomin Yue wrote:
Yes, lh.pial exists
Xiaomin
On Dec 10, 2014, at 10:33 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
it only looks for that if it can't find lh.pial. Does that exist?
On Wed, 10 Dec 2014, Xiaomin Yue wrote:
Hi Bruce,
the mris_thickness was looking for ?h.gray file to run correctly. But no
such file exists. The freesurfer used is 5.3. Any ideas?
The command line is: mris_thickness test_DB48 lh lh.thickness
The error: reading gray matter surface
/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray
MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not
open file.
Thanks,
Xiaomin
____________________________________________________________________________
From: yu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness from pial and white
Date: Wed, 10 Dec 2014 02:47:02 +0000
Thanks. I will try mris_fill.
Xiaomin
From: Bruce Fischl
Sent: Tuesday, December 9, 2014 4:31 PM
To: Freesurfer support list
it creates a file in curvature format, yes. Did you try mris_fill for the
wm.mgz? It won't be exactly the same as the one we would generate. You
could use mris_fill to generate the interior of the ?h.white surface,
then use the aseg to remove non-wm voxels I guess
On Tue, 9 Dec 2014,
Xiaomin Yue wrote:
Thanks very much. Does this create curvature file? Again, is it possible
to generate wm.mgz from those files?
Thanks,
Xiaomin
On Dec 9, 2014, at 4:19 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
I think just the ?h.white and ?h.pial
cheers
Bruce
On Tue, 9 Dec 2014, Xiaomin Yue wrote:
What I mean by inputs is the default files the mris_thickness will be
looking for to run correctly
Xiaomin
On Dec 9, 2014, at 1:08 PM, Xiaomin Yue <yu...@hotmail.com> wrote:
Hi Bruce,
Thanks for your response. What's the inputs to the
mris_thickness? I need the wm.mgz to generate the ratio of gray
vs. white matter.
Xiaomin
Date: Tue, 9 Dec 2014 09:55:21 -0500
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness from pial and white
the thickness you can generate using mris_thikness. Why do you want to
generate a wm.mgz? I guess you could from the wmparc
On Mon, 8 Dec 2014, Xiaomin Yue wrote:
Hi All,
Cortical surface reconstructed using caret from a high resolution MRI
data
(0.25 mm) has been converted to freesurfer format, and viewed correctly
using freeview. My questions are whether it is possible to generate 1)
a
?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using
?h.pial a
nd
?h.white
Thanks very much for your inputs.
Xiaomin
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