Google finds this: 

https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01081.html

Matt. 

On 3/2/18, 1:06 PM, "Kwan-Jin Jung" <kjj...@umass.edu> wrote:

>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
>>>
>>
>


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