On Ubuntu 14.04 what happens if you do ldd mris_make_surfaces?



On 3/2/18, 12:41 PM, "Kwan-Jin Jung" <kjj...@umass.edu> wrote:

>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: ncerr"
>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
>>"${CARET7DIR}/wb_command -set-structure "$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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