Hello,
I am new to using FreeSurfer, and need a little help. I have downloaded and installed FS 2 days ago (from https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall ). To verify the installation I proceeded with all steps on the first page, and everything worked fine.
Then I decided to try the hippo campal segmentation, and I tried the scripts on the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation?hi ghlight=%28hippo%29 . Running the first script
recon-all -s bert -all -hippo-subfields
resulted in a 20+ hour run of FS which completed successfully. Then I started the
kvlQuantifyHippocampalSubfieldSegmentations.sh
to analyze the bert results, and it died on me. I looked into the errors and into the script itself using an editor, and I found out that the script wants to descend (or "cd") into some folders named "left" and "right". However, running the "recon-all" script on the test subject bert (from above) did not generate "left" and "right" folders at all. I looked through the archived messages and did not find an answer to my issue.
Can you help me out here? Is this a known bug and are there updated scripts that I should maybe download? The output of the kvlQuantifyHippocampalSubfieldSegmentations.sh script is provided below
Thank you in advance
Boris Marendic
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OUTPUT OF THE SCRIPT kvlQuantifyHippocampalSubfieldSegmentations.sh
kvlQuantifyHippocampalSubfieldSegmentations.sh /home/freesurfer/subjects
resultsDirectory /home/freesurfer/subjects
cd /home/freesurfer/subjects
numberOfSubjects: 12
resultsDirectory /home/freesurfer/subjects
startIndex: 1
endIndex: 12
Sides to evaluate: left right
Current subject: bert/
cd bert/
Quantifying subject bert/ left
Doing left side
cd left
/home/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: cd : left: No such file or directory
failed to do cd left