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Hello FreeSurfer users,
I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early:
/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found
When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, kvlAutoCrop.bin was located there, as expected. When I tried to run the step manually, it produced the correct output, but the next step gave me the similar error: command not found. I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other binaries were there, as well. The binaries are correctly exported on my PATH. I also made sure to download the Matlab compiler runtime and made sure they were on my PATH.
I am running freesurfer on a Linux machine with the RedHat 7.5 OS.Any help is greatly appreciated.
Thanks, Ryan