I¹m not sure we support the HCP Pipelines on Mac OS X.  You definitely
need to be using a bash interpreter.

What issues were you having on Ubuntu?



On 3/2/18, 10:13 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Kwan-Jin Jung" <hcp-users-boun...@humanconnectome.org on behalf of
kjj...@umass.edu> wrote:

>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 Œcp¹ which needs to be replaced into Œrsync¹ 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
>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
>HCP-Users mailing list

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