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
