External Email - Use Caution        

Hi Juan and Bruce,

I wanted to follow up on my previous email. Do you have any recommendations to manually or automatically fix poor segmentations?

Thank you,
Franchesca

Franchesca Kuhney, M.A. (she/her)
Clinical Psychology Doctoral Student
University of Illinois at Chicago
Behavioral Sciences Building | Rm 3019
1007 W. Harrison St. | Chicago, IL 60607

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On Mon, Jul 19, 2021 at 9:54 AM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Definitely an ASEG problem that the subfield routine couldn’t recover from.
Bruce: any ideas on what may have gone wrong?
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On Jul 17, 2021, at 23:46, Franchesca Kuhney <fkuhne2@uic.edu> wrote:

        External Email - Use Caution        


I hope this is helpful, thank you!

Franchesca Kuhney, M.A. (she/her)
Clinical Psychology Doctoral Student
University of Illinois at Chicago
Behavioral Sciences Building | Rm 3019
1007 W. Harrison St. | Chicago, IL 60607
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On Tue, Jul 13, 2021 at 10:46 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Wow that is indeed terrible. Do you think you could send us the same sagittal slice for aseg.mgz, please?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On Jul 13, 2021, at 22:31, Franchesca Kuhney <fkuhne2@uic.edu> wrote:

        External Email - Use Caution        


Hi Juan,

So sorry for the delay. Attached is an example image. Thanks!

Best,
Franchesca

Franchesca Kuhney, M.A. (she/her)
Clinical Psychology Doctoral Student
University of Illinois at Chicago
Behavioral Sciences Building | Rm 3019
1007 W. Harrison St. | Chicago, IL 60607
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On Fri, Jul 9, 2021 at 1:49 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear Franchesca,
Could you please attach some images illustrating the problem?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On Jul 9, 2021, at 13:06, Franchesca Kuhney <fkuhne2@uic.edu> wrote:

        External Email - Use Caution        


Hello,

I've run into an issue with the longitudinal hippocampus/amygdala segmentation (segmentHA_T1_long.sh). All of the commands ran properly and I got the outputs listed on the FreeSurfer wiki but, upon QAing the segmentations, I realized that a few subjects hippocampal segmentations were a poor fit. It appears that the segmentation includes their parahippocampal gyrus. I'm wondering if you have any recommendations for how to fix these either manually or automatically? Thank you!

Kindly,
Franchesca

Franchesca Kuhney, M.A. (she/her)
Clinical Psychology Doctoral Student
University of Illinois at Chicago
Behavioral Sciences Building | Rm 3019
1007 W. Harrison St. | Chicago, IL 60607
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