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?highlight=%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