Hello,

I am trying to use the segmentHA_T1_long.sh command on my longitudinal data. I have already run all the previous steps and have even successfully run longHippoSubfieldsT1.sh. However I want to use the segmentHA version to get my hippocampal segmentations.

I assume the issue has something to do with the script not being in the FS6.0 version I downloaded? When looking at the literature for installation all I could find was info on installing runtime which I already have. 

Any help debugging the issue would be greatly appreciated.

Below is the code I ran.

#!/bin/tcsh

setenv FREESURFER_HOME /Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.csh

foreach subj (MCIP0031 MCIP0032 MCIP0033 MCIP0035 MCIP0036 MCIP0041 MCIP0048 MCIP0052 MCIP0053 MCIP0054 MCIP0055 MCIP0058 MCIP0061)

setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_MCIP

segmentHA_T1_long.sh base_${subj}

end

I get the following error.

[hlhp-105:/Volumes/DANIEL/freesurfer_MCIP] administrator% ./recon-all_longitudinal_hippo.sh 

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

segmentHA_T1_long.sh: Command not found.

Best,

Daniel Callow

PhD Student, Neuroscience and Cognitive Science

Exercise for Brain Health Lab

University of Maryland, College Park

ddcc2442@gmail.com

443-254-6298