Can you upload one of your problematic subjects? Follow these instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.

On 10/9/2019 5:29 PM, Marina Fernández wrote:

External Email - Use Caution

Dear Douglas,

Thank you very much for the help. We could solve the problem with that subject but now we have a similar problem with another subject. In the previous case, we have only one problematic voxel in the skull, but now the label 75 (it shouldn't exist either) is taking a lot of voxels in the ventricles and the caudate. So, I think that we should use other solution to fix it.

I know that this issue is weird. We use gtmseg command with more or less 500 subjects and we only have this type of problem with two subjects.

Best regards, Marina.

Probably the easiest thing is just to edit that voxel to be one of the neighboring segments. First, load the aseg and find that voxel. See which segment(s) are around that voxel and get the segmentation id. Then run mri_binarize --replaceonly 229 YourNewSegID --i aparc+aseg.mgz --o aparc+aseg.mgz then re-run gtmseg

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