Dear Xin,

Please follow the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

The new command is: segmentHA_T1_long.sh <baseID>  [SUBJECTS_DIR]

Kind regards,

Eugenio

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 Xin Qi <xinqi2000@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, February 7, 2021 at 10:07
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Can't find longHippoSubfieldsT1.sh

        External Email - Use Caution        

Dear Freesurfer Community,
 
I ran the Freesurfer longitudinal pipeline for my subjects (1.5T, T1_data, 6 timepoints each). Now I want to continue with the longitudinal segmentation of hippocampal 
subfields:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields
 
However, when I want to run the command: 
longHippoSubfieldsT1.sh <baseID>
 
I get the error message "bash: longHippoSubfieldsT1.sh: command not found"
 
First thing I did, was checking the Freesurfer folder for the longHippo..sh file.
I am using FS 7.0 but the file is not available.
 
So my questions: where can I get the file longHippoSubfieldsT1.sh or what else can I do to proceed with the HC subfield segmentation?
 
Thanks a lot for your support and looking forward to your reply.
Best
Xin