Hi Arsenije,
If you've already tested out different watershed thresholds and gcut, then yes, the next step would be to manually erase these voxels and reprocess. The ventricle labeling is a separate problem - which version of FreeSurfer are you running? Best, Emma --------- Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Arsenije Subotic <arsenije.subot...@ucalgary.ca> Sent: Tuesday, November 28, 2017 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Erroneous output after recon-all: Bad segmentation and surfaces Dear experts, I recently finished processing a subject for whom I had performed a skull-strip on the brainmask.mgz volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following command as the troubleshooting tutorial suggested to regenerate the surfaces based on the new brainmask.mgz volume: recon-all -autorecon-pial -subjid <subject name> However, after the subject finished processing the surfaces were generated/outlined on the dura as well. I tried performing a g-cut command but it did not get rid of the dura. I also had issues with the subcortical segmentation as the ventricles were not completely segmented. I've attached screenshots for you to see as well. Would it be necessary to manually erase the extra dura and then re-process the subject? Please let me know. Thank you for your help. Best, Arsenije
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