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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