Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS
Hi Matthew, Thank you. It is a long list: linux-vdso.so.1 => (0x7ffece4f) libz.so.1 => /usr/local/lib/libz.so.1 (0x7fafe4dd9000) libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x7fafe4ba1000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7fafe499d000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x7fafe478) libnetcdf.so.6 => /usr/lib/x86_64-linux-gnu/libnetcdf.so.6 (0x7fafe443f000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x7fafe40bd000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fafe3db4000) libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x7fafe3b92000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x7fafe397c000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fafe35b2000) /lib64/ld-linux-x86-64.so.2 (0x7fafe4ff3000) libhdf5_hl.so.6 => /usr/lib/x86_64-linux-gnu/libhdf5_hl.so.6 (0x7fafe3392000) libhdf5.so.6 => /usr/lib/x86_64-linux-gnu/libhdf5.so.6 (0x7fafe2ef5000) libcurl.so.4 => /usr/lib/x86_64-linux-gnu/libcurl.so.4 (0x7fafe2c86000) libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 (0x7fafe2a83000) libidn.so.11 => /usr/lib/x86_64-linux-gnu/libidn.so.11 (0x7fafe285) librtmp.so.1 => /usr/lib/x86_64-linux-gnu/librtmp.so.1 (0x7fafe2634000) libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x7fafe23cb000) libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x7fafe1f87000) libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x7fafe1d3d000) liblber-2.4.so.2 => /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2 (0x7fafe1b2e000) libldap_r-2.4.so.2 => /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2 (0x7fafe18dd000) libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 (0x7fafe16d5000) libgnutls.so.30 => /usr/lib/x86_64-linux-gnu/libgnutls.so.30 (0x7fafe13a5000) libhogweed.so.4 => /usr/lib/x86_64-linux-gnu/libhogweed.so.4 (0x7fafe1172000) libnettle.so.6 => /usr/lib/x86_64-linux-gnu/libnettle.so.6 (0x7fafe0f3c000) libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10 (0x7fafe0cbc000) libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3 (0x7fafe09ea000) libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3 (0x7fafe07bb000) libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x7fafe05b7000) libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0 (0x7fafe03ac000) libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x7fafe0191000) libsasl2.so.2 => /usr/lib/x86_64-linux-gnu/libsasl2.so.2 (0x7fafdff76000) libgssapi.so.3 => /usr/lib/x86_64-linux-gnu/libgssapi.so.3 (0x7fafdfd35000) libp11-kit.so.0 => /usr/lib/x86_64-linux-gnu/libp11-kit.so.0 (0x7fafdfad1000) libtasn1.so.6 => /usr/lib/x86_64-linux-gnu/libtasn1.so.6 (0x7fafdf8be000) libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x7fafdf6ba000) libheimntlm.so.0 => /usr/lib/x86_64-linux-gnu/libheimntlm.so.0 (0x7fafdf4b1000) libkrb5.so.26 => /usr/lib/x86_64-linux-gnu/libkrb5.so.26 (0x7fafdf227000) libasn1.so.8 => /usr/lib/x86_64-linux-gnu/libasn1.so.8 (0x7fafdef85000) libhcrypto.so.4 => /usr/lib/x86_64-linux-gnu/libhcrypto.so.4 (0x7fafded52000) libroken.so.18 => /usr/lib/x86_64-linux-gnu/libroken.so.18 (0x7fafdeb3c000) libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6 (0x7fafde934000) libwind.so.0 => /usr/lib/x86_64-linux-gnu/libwind.so.0 (0x7fafde70b000) libheimbase.so.1 => /usr/lib/x86_64-linux-gnu/libheimbase.so.1 (0x7fafde4fc000) libhx509.so.5 => /usr/lib/x86_64-linux-gnu/libhx509.so.5 (0x7fafde2b1000) libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x7fafddfdc000) 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" <kj
Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS
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
Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS
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
[HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS
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 ‘cp’ which needs to be replaced into ‘rsync’ 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
