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.
I saw there was a question on this topic already, but couldn't find answers: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s...
Thanks, Manorama
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.
I saw there was a question on this topic already, but couldn't find answers: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s...
Thanks, Manorama
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
I saw there was a question on this topic already, but couldn't find answers: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s...
Thanks, Manorama
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
I saw there was a question on this topic already, but couldn't find answers: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s...
Thanks, Manorama
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I read that the option "-thickness" expands the surface by a fraction of its thickness. https://miykael.github.io/nipype/interfaces/generated/interfaces.freesurfer/...
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020 6:25 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.
I saw there was a question on this topic already, but couldn't find answers: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s...
Thanks, Manorama
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/...
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Friday, September 18, 2020 11:01 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020 6:25 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.
I saw there was a question on this topic already, but couldn't find answers: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s...
Thanks, Manorama
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That helped! Thank you so much! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu Sent: Friday, September 18, 2020 6:31 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Make BEM with corrected brainmask
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/...
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Friday, September 18, 2020 11:01 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020 6:25 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.
I saw there was a question on this topic already, but couldn't find answers: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s...
Thanks,
Manorama
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N. Greve
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Fischl, Bruce -
Kadwani, Manorama