Thank you Michael and Donna,
I'm kind of suprised to be running into this error as I've successfully
run HCP on >70 participants so far, and only now I am getting the error.
Perhaps I should say that I installed Freesurfer version 6 (development
version) alongside it once, but all the paths were kept to point to the
old version.
Could that still have caused a problem?
Best wishes,
Barbara
On 31/05/2016 16:49, Harms, Michael wrote:
If running recon-all directly worked fine, that then suggests that
something isn’t set up correctly in your environment when you go to
run the HCP Pipeline scripts.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: [email protected]
From: <[email protected]
<mailto:[email protected]>> on behalf of "Dierker,
Donna" <[email protected] <mailto:[email protected]>>
Date: Tuesday, May 31, 2016 at 9:30 AM
To: Barbara Kreilkamp <[email protected]
<mailto:[email protected]>>, "[email protected]
<mailto:[email protected]>" <[email protected]
<mailto:[email protected]>>
Subject: Re: [HCP-Users] [SPAM] ERROR: mpr2mni305 failed in
FreesurferPipelineBatch.sh
Hi Barbara,
It looks like there was a problem with a runtime library Freesurfer
needs. Have a look at this similar issue:
https://www.mail-archive.com/[email protected]/msg40092.html
I'd report your issue to the Freesurfer mailing list:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport
Hopefully there is a fix that won't be too painful.
Donna
------------------------------------------------------------------------
*From:* [email protected]
<mailto:[email protected]>
<[email protected]
<mailto:[email protected]>> on behalf of Barbara
Kreilkamp <[email protected] <mailto:[email protected]>>
*Sent:* Tuesday, May 31, 2016 3:36:30 AM
*To:* [email protected] <mailto:[email protected]>
*Subject:* [SPAM] [HCP-Users] ERROR: mpr2mni305 failed in
FreesurferPipelineBatch.sh
Dear HCP experts,
I am running freesurfer-Darwin-lion-stable-pub-v5.3.0 on MAC 10.10.5.
Could you please help me with this error message? I think it relates
to the library, this is what it states in talairach_avi.log.
Running recon-all directly worked, but after that I am missing some
files that are needed in PostFreesurferPipelineBatch.sh
But I am unsure how to solve this issue.
Any help is greatly appreciated,
Thank you very much,
Barbara
#@# Talairach Sat May 28 14:18:53 CEST 2016
/Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri
\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
--no-rescale --i orig.mgz --o orig_nu.mgz \n
\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11
18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64
recon-all -s REF088c exited with ERRORS at Sat May 28 14:19:12 CEST 2016
For more details, see the log file
/Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/scripts/recon-all.log
To report a problem, see
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
talaraich_avi.log output
/Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri
/Applications/freesurfer/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11
18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64
Sat May 28 13:27:28 CEST 2016
mri_convert orig_nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from orig_nu.mgz...
crypt_gkey = FSaWN44YqKOYA
TR=8.21, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to talsrcimg.img...
crypt_gkey = FSaWN44YqKOYA
Analyze Output Matrix
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -146.00000;
0.00000 -1.00000 0.00000 148.00000;
0.00000 0.00000 0.00000 1.00000;
--------------------
INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Sat May 28 13:27:29 CEST 2016
/Applications/freesurfer/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $
target=711-2C_as_mni_average_305
---------------------------------------------------------------------
analyzeto4dfp talsrcimg -O0 -y
---------------------------------------------------------------------
$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
Sat May 28 13:27:30 2016
Writing: talsrcimg.4dfp.hdr
$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
Reading: talsrcimg.hdr
header size 348 bytes
hdr.dime.datatypeoffset=70value=2
hdr.dime.bitpixoffset=72value=8
hdr.hist.orientoffset=252value=-1
dimensionality 4
dimensions 256 256 256 1
Reading: talsrcimg.img
Writing: talsrcimg.4dfp.img
Writing: talsrcimg.4dfp.ifh
ifh2hdr talsrcimg -r0to255
ori=2
---------------------------------------------------------------------
gauss_4dfp talsrcimg 1.1
---------------------------------------------------------------------
dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib
Referenced from: /Applications/freesurfer/bin/gauss_4dfp
Reason: image not found
Trace/BPT trap
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133
ERROR: mpr2mni305 execution aborted
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