Hi Matthew,

Since the FreeSurfer HCP version is available for MacOS, I assumed that the HCP 
pipeline is supported in MacOS.

The problems with Ubuntu (both 16.04 and 14.04) were about the missing 
libraries during mris: Libnetcdf.so.6 error during mris_make_surfaces.

This was resolved by following the instruction by Tim: 

But I have the following message during FreeSurferPielineBatch.mine.sh:
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgzrecon-all -s 100307 exited with ERRORS at Fri Mar  2 
13:21:24 EST 2018"

"mris_make_surfaces: symbol lookup error: mris_make_surfaces: undefined symbol: 

On Centos (both 5 and 6), I was getting different errors.

At this point I gave up ...

On Macbook, it ran without these issues until the 'wb_command' problem.

Kwan-Jin Jung, Ph.D.
S230J, HMRC, Life Science Laboratories
UMASS Amherst
Office: 413-577-0538
Website: http://www.umass.edu/ials/hmrc

-----Original Message-----
From: Glasser, Matthew [mailto:glass...@wustl.edu] 
Sent: Friday, March 02, 2018 11:16 AM
To: Kwan-Jin Jung <kjj...@umass.edu>; hcp-users@humanconnectome.org
Cc: Hae-Min Jung <hae-min.j...@austenriggs.net>
Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

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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