Hi,

After I failed to run FreeSurfer pipeline on both Ubuntu and Centos, I tried it 
on MacBook.

It runs without library issues, but it seems to have differences in shell 
scripting commands.

The first example is ‘cp’ which needs to be replaced into ‘rsync’ in both 
FreeSurferHiresWhite.sh and FreeSurferHiresPial.sh.

Then there was another issue in FreeSurferHiresPial.sh at the line #92 of:
"${CARET7DIR}/wb_command -set-structure "$surfdir"/lh.white.surf.gii 
CORTEX_LEFT"

I converted this into:
"open -a ${CARET7DIR}/wb_command -set-structure "$surfdir"/lh.white.surf.gii 
CORTEX_LEFT"

However, I am getting an error of:
"The file /Users/kjjung/MRI/HCP/Practice/CORTEX_LEFT does not exist."

Does any one know how to fix this issue?

My MacBook is macOS High Sierra, v10.13.3.

Kwan-Jin Jung
UMASS Amherst

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