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Sorry,
I realized I did not have the path to freesurfer in my script set to
the dev version. It was set to the FS6.0 version.
Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com <ddcc2...@gmail.com>*
443-254-6298
On Sat, Mar 23, 2019 at 4:39 PM Daniel Callow <ddcc2...@gmail.com> wrote:
> 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
> *ddcc2...@gmail.com <ddcc2...@gmail.com>*
> 443-254-6298
>
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