Hi Stef

It’s really hard to say without seeing the data. We do have a topology fixing tutorial you can go through. If most of the wm.mgz is correct you likely need to find the source of the defect and correct it. You can load the ?h.defect_labels onto the ?h.orig.nofix and/or ?h.inflated.nofix to see where the defective vertices are. Make sure to set the overlay thresholds to 0 so you can see all of them!
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Stef Meliss
Sent: Tuesday, March 23, 2021 9:38 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Some brain area missing after running recon-all

External Email - Use Caution

Hi Bruce,

Thanks so much for your quick reply. Indeed, the area is still present in the ?h.orig.nofix but not in the ?h.orig. Most of the wm.mgz voxels that are included in ?h.orig.nofix, but not in ?h.orig have intensities above 100, but some are as low as 86. Additionally, it also looks to me as if wm.mgz is also missing some voxels. What kind of intervention would you recommend?

Many thanks,

Stef

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 22 March 2021 at 17:16
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Some brain area missing after running recon-all

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

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