Hi again,

First, make a copy of wmparc.mgz, in case something goes wrong.

Then:

% read aseg

aseg=MRIread('aseg.presurf.mgz')

% read wmparc

wmparc=MRIread('wmparc.mgz')

% inpaint hippocampi in wmparc with closes neighboring label

wmparc_inpainted = inpaint(wmparc.vol, wmparc.vol == 17 | wmparc.vol=53);

% paint your own hippocampi on top

wmparc_inpainted(aseg.vol==17)=17;

wmparc_inpainted(aseg.vol==53)=53;

% write results

wmparc.vol= wmparc_inpainted;

MRIwrite(wmparc,’wmparc.mgz’);

You’ll need the attached function inpaint.m.

Cheers,

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: Thursday, July 9, 2020 at 21:06
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

External Email - Use Caution

Hi Eugenio,

Sorry! Can you specify how to copy the edits from aseg to wmparc within Matlab?

aseg=MRIread('aseg.presurf.mgz')

wmparc=MRIread('wmparc.mgz')

asegHC=find(aseg.vol == 17 | aseg.vol=53)

How would I then replace the data corresponding to the HC labels within wmparc with that of asegHC?

Thank you!

Jenna

From: Jenna Katherine Blujus <jkblujus@uwm.edu>
Sent: Wednesday, July 8, 2020 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: Freesurfer Hippocampal Subfield Misalignment

Hi Eugenio,

Great, thank you! One last question - after I edit the aseg and wmparc files would you recommend that I only rerun the recon-all hippocampal-subfields-T2 step or should I rerun certain autorecon steps of recon-all?

Thank you!

Jenna

Jenna K. Blujus, M.S.
Graduate Student
Neurobiology of Aging Laboratory
University of Wisconsin-Milwaukee
jkblujus@uwm.edu

From: Jenna Katherine Blujus <jkblujus@uwm.edu>
Sent: Wednesday, July 8, 2020 10:36 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: Freesurfer Hippocampal Subfield Misalignment

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>
Content-Type: text/plain; charset="utf-8"

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)
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com%2F&data=02%7C01%7Cjkblujus%40uwm.edu%7C3cfb2d05fcb846c4069f08d82351aa41%7C0bca7ac3fcb64efd89eb6de97603cf21%7C1%7C0%7C637298180959768442&sdata=YHDbC41mQEhaCDMkRMPGsj4UE1cG8sLINz6e3xsV0v4%3D&reserved=0

Forward

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