Hi! I meant that if the hippocampus was oversegmented (e.g., over the amygdala), you’d still have to paint new labels in those regions (as amygdala, in our example).
You could use the Matlab functions under $FREESURFER_HOME/matlab (in particular MRIread and MRIwrite) to programmatically move the edits from aseg.mgz to wmparc.mgz.
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus@uwm.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, July 8, 2020 at 11:37
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
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Hi Eugenio,
Thank you for the tips! This has happened to a number of my subjects but I have finished editing the HC label in their aseg files. How would I copy the HC from aseg.mgz to wmparc.mgz? Can you clarify
what you mean by "you still need to fix the surrounding labels"?
Thank you,
Jenna
Message: 3
Date: Tue, 7 Jul 2020 20:53:12 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <85489126-5DC1-4464-810B-01A7E825895A@mgh.harvard.edu>
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Dear Jenna,
1.Manually editing aseg.mgz fixes the initialization (super important).
2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important)
If it?s only 1 subject in a bigger study, I?d probably call it a QC fail and leave it out.
If it?s a single case you?re very interested in, I would edit both aseg.mgz and wmparc.mgz (you can copy the hippocampus from one into the other, but you still need to fix the surrounding labels).
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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Jenna K. Blujus, M.S.
Graduate Student
Neurobiology of Aging Laboratory
University of Wisconsin-Milwaukee
jkblujus@uwm.edu
From: Jenna Katherine Blujus
Sent: Tuesday, July 7, 2020 3:23 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Hippocampal Subfield Misalignment
Hi Experts,
I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output
to the anatomical boundaries of the hippocampus in some of my subjects is off. For example, the left hippocampal subfield segmentation in one subject is superior and medial to the hippocampus. I checked the aseg.presurf file (since I am using v6.0) and indeed
the whole left hippocampus is off.
I saw in a previous thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23942.html) that
it was suggested to edit the hippocampal segmentation within the aseg file to potentially improve alignment of the subfield segmentation. However, a more recent post (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54543.html)
stated that both the wmparc.mgz and aseg.mgz files would need to be edited and that this was not recommended. Do you have any recommendations on how to move forward? I did edit the hippocampal segmentation within the aseg.presurf file in one of my subjects
and reran the subfield segmentation command which substantially improved the output (i.e., it overlays on the hippocampus after correction). Would you suggest that I continue with editing the aseg using previously published protocols on segmenting the hippocampus
by hand or would you recommend something else?
Thanks in advance!
Jenna