I was running into issues processing subjects, with errors just getting through the autorecon1 step of the pipeline. My terminal outputs the following:
/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri
/usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Tue Jan 10 12:53:44 EST 2017
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
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.129237
/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.32349e-23, -1.32349e-23)
j_ras = (0, 1.49012e-08, -1)
k_ras = (0, 1, 1.49012e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.129237/nu0.mnc...
--------------------------------------------------------
Iteration 1 Tue Jan 10 12:53:47 EST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.129237/nu0.mnc ./tmp.mri_nu_correct.mni.129237/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.129237/0/ -iterations 1000 -distance 50
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/pkg/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
Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 10007 exited with ERRORS at Tue Jan 10 12:53:47 EST 2017
For more details, see the log file /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/scripts/recon-all.log