Hi Matthew, Thank you. It is a long list: linux-vdso.so.1 => (0x00007ffece4f0000) libz.so.1 => /usr/local/lib/libz.so.1 (0x00007fafe4dd9000) libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x00007fafe4ba1000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fafe499d000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fafe4780000) libnetcdf.so.6 => /usr/lib/x86_64-linux-gnu/libnetcdf.so.6 (0x00007fafe443f000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fafe40bd000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fafe3db4000) libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fafe3b92000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fafe397c000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fafe35b2000) /lib64/ld-linux-x86-64.so.2 (0x00007fafe4ff3000) libhdf5_hl.so.6 => /usr/lib/x86_64-linux-gnu/libhdf5_hl.so.6 (0x00007fafe3392000) libhdf5.so.6 => /usr/lib/x86_64-linux-gnu/libhdf5.so.6 (0x00007fafe2ef5000) libcurl.so.4 => /usr/lib/x86_64-linux-gnu/libcurl.so.4 (0x00007fafe2c86000) libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 (0x00007fafe2a83000) libidn.so.11 => /usr/lib/x86_64-linux-gnu/libidn.so.11 (0x00007fafe2850000) librtmp.so.1 => /usr/lib/x86_64-linux-gnu/librtmp.so.1 (0x00007fafe2634000) libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00007fafe23cb000) libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00007fafe1f87000) libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007fafe1d3d000) liblber-2.4.so.2 => /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2 (0x00007fafe1b2e000) libldap_r-2.4.so.2 => /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2 (0x00007fafe18dd000) libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 (0x00007fafe16d5000) libgnutls.so.30 => /usr/lib/x86_64-linux-gnu/libgnutls.so.30 (0x00007fafe13a5000) libhogweed.so.4 => /usr/lib/x86_64-linux-gnu/libhogweed.so.4 (0x00007fafe1172000) libnettle.so.6 => /usr/lib/x86_64-linux-gnu/libnettle.so.6 (0x00007fafe0f3c000) libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10 (0x00007fafe0cbc000) libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007fafe09ea000) libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007fafe07bb000) libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007fafe05b7000) libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007fafe03ac000) libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007fafe0191000) libsasl2.so.2 => /usr/lib/x86_64-linux-gnu/libsasl2.so.2 (0x00007fafdff76000) libgssapi.so.3 => /usr/lib/x86_64-linux-gnu/libgssapi.so.3 (0x00007fafdfd35000) libp11-kit.so.0 => /usr/lib/x86_64-linux-gnu/libp11-kit.so.0 (0x00007fafdfad1000) libtasn1.so.6 => /usr/lib/x86_64-linux-gnu/libtasn1.so.6 (0x00007fafdf8be000) libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007fafdf6ba000) libheimntlm.so.0 => /usr/lib/x86_64-linux-gnu/libheimntlm.so.0 (0x00007fafdf4b1000) libkrb5.so.26 => /usr/lib/x86_64-linux-gnu/libkrb5.so.26 (0x00007fafdf227000) libasn1.so.8 => /usr/lib/x86_64-linux-gnu/libasn1.so.8 (0x00007fafdef85000) libhcrypto.so.4 => /usr/lib/x86_64-linux-gnu/libhcrypto.so.4 (0x00007fafded52000) libroken.so.18 => /usr/lib/x86_64-linux-gnu/libroken.so.18 (0x00007fafdeb3c000) libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6 (0x00007fafde934000) libwind.so.0 => /usr/lib/x86_64-linux-gnu/libwind.so.0 (0x00007fafde70b000) libheimbase.so.1 => /usr/lib/x86_64-linux-gnu/libheimbase.so.1 (0x00007fafde4fc000) libhx509.so.5 => /usr/lib/x86_64-linux-gnu/libhx509.so.5 (0x00007fafde2b1000) libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007fafddfdc000)
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 2:00 PM To: Kwan-Jin Jung <kjj...@umass.edu>; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS 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