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
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: 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
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
soluti
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: Free
, 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
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
s
(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 - U
y "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-
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 Hip
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 Jen
d.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 shou
abels"?
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>
urfer@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 c
ed 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-01a7e
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
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’r
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