External Email - Use Caution
I have attached the log - is there any chance you could tell me what the problem is?
Thanks,
Ian
Not sure. Can you run this
cd /execute/freesurfer2016/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
and send the terminal output?
On 6/29/2020 7:01 AM, Ian wrote:
External Email - Use Caution
I have attached the log - is there any chance you could tell me what the problem is?
Thanks,
Ian
--
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Here you go Doug, thanks.
docker@7d97b79d7546:/execute/freesurfer2016/mri$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /execute/freesurfer2016/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux 7d97b79d7546 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC 2020 x86_64 GNU/Linux Tue Jun 30 12:13:22 UTC 2020 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.835 /execute/freesurfer2016/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.835/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.835/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=7.92, 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.835/nu0.mnc...
-------------------------------------------------------- Iteration 1 Tue Jun 30 12:13:23 UTC 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.835/nu0.mnc ./tmp.mri_nu_correct.mni.835/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.835/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct
On 29/06/2020 15:50, Douglas N. Greve wrote:
Not sure. Can you run this
cd /execute/freesurfer2016/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
and send the terminal output?
On 6/29/2020 7:01 AM, Ian wrote:
External Email - Use Caution
I have attached the log - is there any chance you could tell me what the problem is?
Thanks,
Ian
--
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do all subjects have this problem or just this one? Have you looked at orig.mgz to rule out any major problems?
On 6/30/20 8:13 AM, Ian wrote:
External Email - Use Caution
Here you go Doug, thanks.
docker@7d97b79d7546:/execute/freesurfer2016/mri$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /execute/freesurfer2016/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux 7d97b79d7546 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC 2020 x86_64 GNU/Linux Tue Jun 30 12:13:22 UTC 2020 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.835 /execute/freesurfer2016/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.835/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.835/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=7.92, 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.835/nu0.mnc...
Iteration 1 Tue Jun 30 12:13:23 UTC 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.835/nu0.mnc ./tmp.mri_nu_correct.mni.835/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.835/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct
On 29/06/2020 15:50, Douglas N. Greve wrote:
Not sure. Can you run this
cd /execute/freesurfer2016/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
and send the terminal output?
On 6/29/2020 7:01 AM, Ian wrote:
External Email - Use Caution
I have attached the log - is there any chance you could tell me what the problem is?
Thanks,
Ian
--
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
*Ian Hardingham*
Chief Technology Officer
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ian.hardingham@oxfordbraindiagnostics.com mailto:terry.pollard@oxfordbraindiagnostics.com
+44 (0)7789 770555
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N. Greve
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Ian