Hi Stef
This is usually the result of a incorrectly fixed topological defect. You can confirm this if the area is present in the ?h.orig.nofix and not in the ?h.orig. The fix depends on the source of the defect. It might be as simple as drawing a single voxel back into the wm.mgz, but might need more. Look at the wm and see if it is mostly accurate or not and whether the intensities in the white matter are near where they should be (target is 110, so ideally mostly above 100)
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Stef Meliss Sent: Monday, March 22, 2021 10:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Some brain area missing after running recon-all
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External Email - Use Caution Dear FreeSurfer Experts
I am using FreeSurfer on my anatomical data to use segmentations and parcellations in my fMRI analyses in AFNI. After reviewing the output from recon-all -all (FreeSurfer version 6.0.0), I noticed that one subject is missing some occipital areas in the output (e.g. aparc+aseg.mgz). Please see attached for a screenshot of the output from
freeview -v mri/brainmask.mgz \ mri/wm.mgz:colormap=heat:opacity=0.4 \ -f surf/lh.white:edgecolor=yellow \ surf/lh.pial:edgecolor=red \ surf/rh.white:edgecolor=yellow \ surf/rh.pial:edgecolor=red \ surf/rh.inflated:visible=0 \ surf/lh.inflated:visible=0
From what I read in the information on troubleshooting the output, I understand that manual editing is necessary to fix this – is this correct? I have verified that the missing areas are included in the brainmask as well as aseg.presurf. I am not sure though how to determine whether I am dealing with a segmentation error or a normalization error or maybe even a combination of both.
If you could give me some pointers on which steps to take, that would be highly appreciated.
Many thanks in advance for your help.
Best regards,
Stef