Hi Elena,
What is the age range of your subjects?
Best, Lilla
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Elana Sarabin
<elana.sarab...@ucalgary.ca>
Sent: Wednesday, July 29, 2020 11:02 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all Soft Errors
External Email - Use Caution
Hi Freesurfer experts,
I am a first time user of FreeSurfer and I haven’t been able to find any
threads for how to fix some of my problems. I have a very large dataset and as
I am editing on freeview I am noticing that ½ or more of my participants have a
large area missing in the brainmask.mgz file but the region is visible from the
T1.file. In some participant scans the areas missing arent too big however
other scans (the photo I attached) have a very large portion of the brain
missing. I have tried quite a few things to fix this including re running
recon-all, adding control points, and adjusting the wsthresh value, however,
none have worked. Wondering if there is a way to fix this kind of error and if
there is a way to prevent this from happening as I run recon-all on future
participants. In addition, I have been duplicating my files before editing in
order to always have the original files as a backup. With some participants
when I duplicate the files their T1.mgz file ends up completely white (image
attached). I have yet to see this in a none duplicated file however with some
participants I can duplicate the files and have no issue. I have attached
photos of both of my problems. Any suggestions for fixes would be greatly
appreciated.
Thanks,
Elana
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