Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
External Email - Use Caution Hi Eugenio, I am having trouble uploading the file through FTP. Can you send me an email to send the file to using the Martinos Center File Drop? Thanks, Jenna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
Hard to tell, Jenna! Please do upload a sample subject using the instructions in the wiki, and I’ll take a look. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Jenna Katherine Blujus Reply to: Freesurfer support list Date: Tuesday, 14 July 2020 at 13:15 To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Eugenio, I might have fixed this particular issue. I ran AFNI's 3dUnifize on the T1 before submitting it to recon-all and this improved the segmentation (it now overlays on the hippocampus). However, I still have some other files that this solution did not work for (see attached picture). I have a few subjects where the segmentation is slightly superior to the hippocampus. Editing the aseg or running 3dUnifize did not fix this issue. Do you have any suggested solutions? Thank you for your help! Jenna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
External Email - Use Caution Hi Eugenio, I might have fixed this particular issue. I ran AFNI's 3dUnifize on the T1 before submitting it to recon-all and this improved the segmentation (it now overlays on the hippocampus). However, I still have some other files that this solution did not work for (see attached picture). I have a few subjects where the segmentation is slightly superior to the hippocampus. Editing the aseg or running 3dUnifize did not fix this issue. Do you have any suggested solutions? Thank you for your help! Jenna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
External Email - Use Caution Hi Eugenio, Yes, I can - which files would you like and where should I upload them? Thanks, Jenna From: Jenna Katherine Blujus Sent: Monday, July 13, 2020 6:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer Hippocampal Subfield Misalignment Hi Eugenio, I reran the segmentations after editing the aseg.presurf.mgz files and copying the edited HC to the wmparc.mgz files but the segmentations did not improve. Is there anything else you would suggest to do? Here is an example of one of my subjects. As you can see the left segmentation is not aligned with the left hippocampus. Thanks, Jenna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
Hi Jenna, Would it be posible for you to share the subject? This is very weird. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Jenna Katherine Blujus Reply-To: Freesurfer support list Date: Monday, July 13, 2020 at 19:29 To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Eugenio, I reran the segmentations after editing the aseg.presurf.mgz files and copying the edited HC to the wmparc.mgz files but the segmentations did not improve. Is there anything else you would suggest to do? Here is an example of one of my subjects. As you can see the left segmentation is not aligned with the left hippocampus. Thanks, Jenna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
External Email - Use Caution Hi Eugenio, I reran the segmentations after editing the aseg.presurf.mgz files and copying the edited HC to the wmparc.mgz files but the segmentations did not improve. Is there anything else you would suggest to do? Here is an example of one of my subjects. As you can see the left segmentation is not aligned with the left hippocampus. Thanks, Jenna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
Sorry!
function Icropped=applyCropping(I,cropping)
i1=cropping(1);
j1=cropping(2);
k1=cropping(3);
i2=cropping(4);
j2=cropping(5);
k2=cropping(6);
Icropped=I(i1:i2,j1:j2,k1:k2,:,:,:,:,:,:,:,:,:,:);
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Jenna Katherine
Blujus
Reply-To: Freesurfer support list
Date: Friday, July 10, 2020 at 18:32
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
External Email - Use Caution
Hi Eugenio,
Ok, great! The inpaint script requires the applyCropping function. I tried
finding a copy of the function on github but was unsuccessful. Do you have a
copy of the applyCropping function?
Thanks,
Jenna
From: Jenna Katherine Blujus
Sent: Thursday, July 9, 2020 8:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: Freesurfer Hippocampal Subfield Misalignment
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
Sent: Wednesday, July 8, 2020 5:10 PM
To: 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
jkblu...@uwm.edu
From: Jenna Katherine Blujus
Sent: Wednesday, July 8, 2020 10:36 AM
To: 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 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: Freesurfer support list
Message-ID: <85489126-5dc1-4464-810b-01a7e8258...@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%2Fdata=02%7C01%7Cjkblujus%40uwm.edu%7C3cfb2d05fcb846c4069f08d82351aa41%7C0bca7ac3fcb64efd89eb6de97603cf21%7C1%7C0%7C637298180959768442sdata=YHDbC41mQEhaCDMkRMPGsj4UE1cG8sLINz6e3xsV0v4%3Dreserved=0
Reply
Forward
Jenna K. Blujus, M.S.
Graduate Student
Neurobiology of Aging Laboratory
University of Wisconsin-Milwaukee
jkblu...@uwm.edu
From: Jenna Katherine Blujus
Sent: Tuesday, July 7, 2020 3:23 PM
To: 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 withi
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
External Email - Use Caution
Hi Eugenio,
Ok, great! The inpaint script requires the applyCropping function. I tried
finding a copy of the function on github but was unsuccessful. Do you have a
copy of the applyCropping function?
Thanks,
Jenna
From: Jenna Katherine Blujus
Sent: Thursday, July 9, 2020 8:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: Freesurfer Hippocampal Subfield Misalignment
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
Sent: Wednesday, July 8, 2020 5:10 PM
To: 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
jkblu...@uwm.edu
From: Jenna Katherine Blujus
Sent: Wednesday, July 8, 2020 10:36 AM
To: 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 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: Freesurfer support list
Message-ID: <85489126-5dc1-4464-810b-01a7e8258...@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%2Fdata=02%7C01%7Cjkblujus%40uwm.edu%7C3cfb2d05fcb846c4069f08d82351aa41%7C0bca7ac3fcb64efd89eb6de97603cf21%7C1%7C0%7C637298180959768442sdata=YHDbC41mQEhaCDMkRMPGsj4UE1cG8sLINz6e3xsV0v4%3Dreserved=0
Reply
Forward
Jenna K. Blujus, M.S.
Graduate Student
Neurobiology of Aging Laboratory
University of Wisconsin-Milwaukee
jkblu...@uwm.edu
From: Jenna Katherine Blujus
Sent: Tuesday, July 7, 2020 3:23 PM
To: 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
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,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Jenna Katherine
Blujus
Reply-To: Freesurfer support list
Date: Thursday, July 9, 2020 at 21:06
To: "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
Sent: Wednesday, July 8, 2020 5:10 PM
To: 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
jkblu...@uwm.edu
From: Jenna Katherine Blujus
Sent: Wednesday, July 8, 2020 10:36 AM
To: 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 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: Freesurfer support list
Message-ID: <85489126-5dc1-4464-810b-01a7e8258...@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%2Fdata=02%7C01%7Cjkblujus%40uwm.edu%7C3cfb2d05fcb846c4069f08d82351aa41%7C0bca7ac3fcb64efd89eb6de97603cf21%7C1%7C0%7C637298180959768442sdata=YHDbC41mQEhaCDMkRMPGsj4UE1cG8sLINz6e3xsV0v4%3Dreserved=0
Reply
Forward
Jenna K. Blujus, M.S.
Graduate Student
Neurobiology of Aging Laboratory
University of Wisconsin-Milwaukee
jkblu...@uwm.edu
From: Jenna Katherine Blujus
Sent: Tuesday, July 7, 2020 3:23 PM
To: 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 co
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
Sent: Wednesday, July 8, 2020 5:10 PM
To: 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
jkblu...@uwm.edu
From: Jenna Katherine Blujus
Sent: Wednesday, July 8, 2020 10:36 AM
To: 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 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: Freesurfer support list
Message-ID: <85489126-5dc1-4464-810b-01a7e8258...@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%2Fdata=02%7C01%7Cjkblujus%40uwm.edu%7C3cfb2d05fcb846c4069f08d82351aa41%7C0bca7ac3fcb64efd89eb6de97603cf21%7C1%7C0%7C637298180959768442sdata=YHDbC41mQEhaCDMkRMPGsj4UE1cG8sLINz6e3xsV0v4%3Dreserved=0
Reply
Forward
Jenna K. Blujus, M.S.
Graduate Student
Neurobiology of Aging Laboratory
University of Wisconsin-Milwaukee
jkblu...@uwm.edu
From: Jenna Katherine Blujus
Sent: Tuesday, July 7, 2020 3:23 PM
To: 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
Just the subfields ;-) Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Jenna Katherine Blujus Reply-To: Freesurfer support list Date: Wednesday, July 8, 2020 at 18:11 To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution 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 jkblu...@uwm.edu From: Jenna Katherine Blujus Sent: Wednesday, July 8, 2020 10:36 AM To: 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 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment To: Freesurfer support list Message-ID: <85489126-5dc1-4464-810b-01a7e8258...@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%2Fdata=02%7C01%7Cjkblujus%40uwm.edu%7C3cfb2d05fcb846c4069f08d82351aa41%7C0bca7ac3fcb64efd89eb6de97603cf21%7C1%7C0%7C637298180959768442sdata=YHDbC41mQEhaCDMkRMPGsj4UE1cG8sLINz6e3xsV0v4%3Dreserved=0 Reply Forward Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblu...@uwm.edu From: Jenna Katherine Blujus Sent: Tuesday, July 7, 2020 3:23 PM To: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
External Email - Use Caution 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 jkblu...@uwm.edu From: Jenna Katherine Blujus Sent: Wednesday, July 8, 2020 10:36 AM To: 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 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment To: Freesurfer support list Message-ID: <85489126-5dc1-4464-810b-01a7e8258...@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%2Fdata=02%7C01%7Cjkblujus%40uwm.edu%7C3cfb2d05fcb846c4069f08d82351aa41%7C0bca7ac3fcb64efd89eb6de97603cf21%7C1%7C0%7C637298180959768442sdata=YHDbC41mQEhaCDMkRMPGsj4UE1cG8sLINz6e3xsV0v4%3Dreserved=0 Reply Forward Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblu...@uwm.edu From: Jenna Katherine Blujus Sent: Tuesday, July 7, 2020 3:23 PM To: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
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) http://www.jeiglesias.com From: on behalf of Jenna Katherine Blujus Reply-To: Freesurfer support list Date: Wednesday, July 8, 2020 at 11:37 To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution 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 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment To: Freesurfer support list Message-ID: <85489126-5dc1-4464-810b-01a7e8258...@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%2Fdata=02%7C01%7Cjkblujus%40uwm.edu%7C3cfb2d05fcb846c4069f08d82351aa41%7C0bca7ac3fcb64efd89eb6de97603cf21%7C1%7C0%7C637298180959768442sdata=YHDbC41mQEhaCDMkRMPGsj4UE1cG8sLINz6e3xsV0v4%3Dreserved=0 Reply Forward Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblu...@uwm.edu From: Jenna Katherine Blujus Sent: Tuesday, July 7, 2020 3:23 PM To: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
External Email - Use Caution 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 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment To: Freesurfer support list Message-ID: <85489126-5dc1-4464-810b-01a7e8258...@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%2Fdata=02%7C01%7Cjkblujus%40uwm.edu%7C3cfb2d05fcb846c4069f08d82351aa41%7C0bca7ac3fcb64efd89eb6de97603cf21%7C1%7C0%7C637298180959768442sdata=YHDbC41mQEhaCDMkRMPGsj4UE1cG8sLINz6e3xsV0v4%3Dreserved=0 Reply Forward Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblu...@uwm.edu From: Jenna Katherine Blujus Sent: Tuesday, July 7, 2020 3:23 PM To: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
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) http://www.jeiglesias.com *From: * on behalf of Jenna Katherine Blujus *Reply-To: *Freesurfer support list *Date: *Tuesday, July 7, 2020 at 16:24 *To: *"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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
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: on behalf of Jenna Katherine Blujus Reply-To: Freesurfer support list Date: Tuesday, July 7, 2020 at 16:24 To: "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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
