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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
External Email - Use Caution
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
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