That helped! Thank you so much! ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <bfis...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Douglas Greve <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> Sent: Friday, September 18, 2020 11:01 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Wednesday, September 9, 2020 6:25 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto: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=subject:%22%5C%5BFreesurfer%5C%5D+mri_watershed%22&o=newest&f=1 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<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
