Try:

 

mris_expand lh.brainmask.surf 3 inner_skull

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Kadwani, Manorama
Sent: Friday, September 18, 2020 6:16 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Make BEM with corrected brainmask

 

I read that the option "-thickness" expands the surface by a fraction of its thickness.

https://miykael.github.io/nipype/interfaces/generated/interfaces.freesurfer/utils.html#mrisexpand

 

How to expand by distance in mm? I want to expand using distance. But when I use the option "-distance" I get an error that it was an unknown option.

 

If that's not possible I tried using thickness and got this output:

< $ mris_expand -thickness lh.brainmask.surf 3 inner_skull

using distance as a % of thickness

expanding surface lh.brainmask.surf by 300.0% of thickness and writing it to inner_skull

reading thickness...

MRISreadNewCurvature: incompatible vertex number in file ./lh.thickness

No such file or directory

mris_expand: could not load thickness file

No such file or directory >

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edu>
Sent: Friday, September 18, 2020 11:01 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Make BEM with corrected brainmask

 

Try mris_expand

On 9/16/20 10:24 PM, Kadwani, Manorama wrote:

Thank you, I got a brain surface using the mri_binarize function.

Is there a function for expanding the surface radially by a few millimeters? I want to create the inner skull surface as an expansion of the brain surface.

 

Thanks,
Manorama

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, September 9, 2020 6:25 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Make BEM with corrected brainmask

 

I'm not sure, but you might be able to just create a surface from the brain mask with
mri_binarize --i brainmask.mgz --min 0.5 --surf brainmask.surf
You can smooth it a bit if you add --surf-smooth 2
where 2 is the number of iterations (more for smoother)
Try that

On 9/9/2020 6:01 PM, Kadwani, Manorama wrote:

Hi,

 

Why does the "mri_watershed" function create a new brainmask? Is there a way to create BEM surfaces from an existing or already corrected brainmask?

 

I had manually edited the brainmask during recon-all process. After the recon-all process completed, the pial surfaces looked good.

But when I ran 'make_watershed_bem', the BEM surfaces came out incorrect. The function 'mri_watershed' re-created a brainmask with the same errors that I had corrected earlier.

 

 

Thanks,

Manorama 



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