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