Dear Freesurfer experts,


I have processed my subject with recon-all and subfields hippocampal segmentation. . I have tried to use kvlQuantifyHippocampalSubfieldSegmentations.sh on a subset of my subjects. I have these subjects A  B  C  D  E  fsaverage in a folder. When I try to exclude fsaverage by using this command kvlQuantifyHippocampalSubfieldSegmentations.sh  ~/subjects/hippo 1 5.  I get this error message.

cd A/
Quantifying subject A/ left
Doing left side
cd left
/usr/local/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: cd: left: No such file or directory
failed to do cd left
I have issued this command both in tsch and in bash.
However, when I run the command without any options in the same folder, it works but bails out as expected when it reaches fsaverage-

Best regards,

Knut J. Bjuland
PhD candidate
NTNU