Hi Harriet,
Regarding the first screenshot - If the hole is apparent in more than one or two slides, appears in the 3D window, and could be significant to your study, I would recommend manually editing the brainmask.mgz volume.
With regards to the second screenshot - FreeSurfer measures cortical surfaces so it is typical for non-cortical areas, such as around ventricles and the hippocampus, to appear that there are areas unaccounted for. This is not an error. It is possible, however, to edit the segmentation if you are interested.
For more information on FreeSurfer output and how and when to make edits, you can refer to our tutorial wiki pages for further instruction: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0...
Best, Jocelyn
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harriet Cornwell hgc36@bath.ac.uk Sent: Monday, November 9, 2020 11:55 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Editing Issues
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Hi FreeSurfer team,
Here are the details regarding the versions of FreeSurfer that my team are using: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
I have a couple of questions regarding editing.
1. Whilst editing one brain we discovered a small hole (see just above the cursor on Screenshot 1). Does this require any manual editing? If so, what would you recommend we do? 2. We are working with brains that were scanned at multiple sites. FreeSurfer seems to have a problem segmenting around the ventricles (see Screenshot 2) with a number of brains from one of the sites. Is this an issue that requires manual editing and if so, what do you recommend we do?
If you need any further information, please let me know. Thank you in advance for any advice you can offer.
Harriet
PhD Student | University of Bath