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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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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
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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
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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
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
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
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
sj4UE1cG8sLINz6e3xsV0v4%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.
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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
