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
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