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