Dear Dr. Iglesias,

Thank you for your quick response and insight. I wanted to make sure that there were not any specific requirements for the T2w scan when using the segmentation command. I will try both and let you know my thoughts.

Kindly,

Joshua E. Pasaye, B.S. (he/him/his)

Clinical Research Coordinator | Imaging Core

Mesulam Center for Cognitive Neurology and Alzheimer's Disease

Northwestern University – Feinberg School of Medicine

300 E. Superior Street, Tarry 8-734, Chicago, IL 60611

(312) 503-5675 | joshua.pasaye@northwestern.edu

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Date: Friday, November 17, 2023 at 2:48 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

Dear Joshua,

This is a bit of an empirical question. I’d totally run both on a few subjects and compare the results.

If you do so: I would selfishly/greatly appreciate it if you shared your impressions with me :-)

Cheers,

/Eugenio

Juan Eugenio Iglesias

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Joshua Ezequiel Pasaye <joshua.pasaye@northwestern.edu>
Date: Friday, November 17, 2023 at 11:46 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

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Hello,

I am working on project using Freesurfer’s “Segmentation of hippocampal subfields and nuclei of the amygdala” to segment the hippocampal subfields and compare it with a software called ASHS developed by the Penn Image Computing and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w SPC vNav.08 iso,  ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to run the command: segmentHA_T2.sh  bert  FILE_ADDITIONAL_SCAN   ANALYSIS_ID  USE_T1  [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal sequence so to compare the two outputs, it would be ideal to also use the HighRes Hippocampal sequence.