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) http://www.jeiglesias.com
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: Tuesday, July 7, 2020 at 16:24 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
External Email - Use Caution 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
Is the T2 aligned with the T1?
On 7/7/2020 4:53 PM, Iglesias Gonzalez, Juan E. wrote:
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)
*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: *Tuesday, July 7, 2020 at 16:24 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Freesurfer Hippocampal Subfield Misalignment
* External Email - Use Caution *
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
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Iglesias Gonzalez, Juan E.