On Ubuntu 14.04 what happens if you do ldd mris_make_surfaces? Peace,
Matt. 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: >https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04837.html. > >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? > >Peace, > >Matt. > >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: > >>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 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 >>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 >> >>_______________________________________________ >>HCP-Users mailing list >>HCP-Users@humanconnectome.org >>http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
