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
