External Email - Use Caution
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 ddcc2442@gmail.com* 443-254-6298
External Email - Use Caution
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 *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Sat, Mar 23, 2019 at 4:39 PM Daniel Callow ddcc2442@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 *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
freesurfer@nmr.mgh.harvard.edu
-
Daniel Callow