Well you will actually have to run the command on the file to get a meaningful output. Sometimes FreeSurfer has shell wrappers for binaries, so you’ll need to be sure that isn’t the case for mris_make_surfaces, but I don’t think it is.
Peace, Matt. On 3/2/18, 12:58 PM, "Kwan-Jin Jung" <kjj...@umass.edu> wrote: >Hi Matthew, > >jung@FileServer:~/bin/HCP/Examples/Scripts$ ldd mris_make_surfaces >ldd: ./mris_make_surfaces: No such file or directory > > >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 1:45 PM >To: Kwan-Jin Jung <kjj...@umass.edu>; hcp-users@humanconnectome.org >Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS > >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
