Dear Sunah,

I would use the T1 alone.

Cheers,

/E

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 최선아 / 학생 / 뇌인지과학과 <kis02204@snu.ac.kr>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, September 14, 2020 at 03:16
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Segmentation of hippocampus and amygdala: using an additional scan with low-pixel

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Hello FreeSurfer Developers,

I am attempting a quality check for my segmentation using an additional scan. My segmentation of hippocampal subfields and nuclei of the amygdala using an additional scan were successfully done. However, I am not sure it is better to use an additional scan since its pixel density is low. I used a T1 image with 0.977*0.977*1(mm, x*y*z axis) pixel, and T2 FLAIR image with 0.688*0.688*6(mm, x*y*z axis) pixel. Is it okay to use an additional scan having a big pixel size such as 6mm? Can I still say that the segmentation with the additional scan is more reliable than solely using a T1 scan? I checked the outputs using freeview, but it was difficult to conclude. 

1) Freesurfer version: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b

2) Platform: Ubuntu 18.04 LTS

Thanks for your help.

Thanks.

Sunah.