Re: [Freesurfer] No voxel in mask using mri_binarize

The problem is probably the --erode 1. Cortex is very thin, so eroding by even one voxel may eliminate the entire ROI. Also, I'm not sure what the commas in the segmentation numbers will do

On 8/17/14 9:11 AM, wang kangcheng wrote:

Dear experts I want to create a mask for prefrontal gyrus. I used labels ( 1001, 1003, 1012,1014,1018 etc,)in FreeSurferColorLUT.txt and run the command like following mri_binarize --i con_sub01/mri/aparc.a2009s+aseg.mgz --out segment.nii.gz --match 1001, 1003, 1012,1014,1018 ----erode 1

But it found 0 voxels in final mask. How should I do ?

Thank you

---

Wang Kangcheng

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer