Hello everybody,
I have searched the mailing list and I have found the same error I am facing but unfortunately I haven't been able fo find the correct answer.
I am running Freesurfer 6.0 on Debian 8.0 (Neurodebian).
When I run recon-all I get the following output, which I also attach in a text file (recon-all.log)
I am new to Freesurfer, sorry for the inconvenience, I would appreciate very much if someone could point me in the right direction,
Thank you,
Jordi
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Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer Actual FREESURFER_HOME /usr/local/freesurfer Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/scripts/recon-all.local-copy' /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018
mri_convert /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/20180305_081619SAGT1SENSE14RECON1s1201a1012.nii.gz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz
mri_convert.bin /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/20180305_081619SAGT1SENSE14RECON1s1201a1012.nii.gz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/20180305_081619SAGT1SENSE14RECON1s1201a1012.nii.gz... TR=9.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0917001, -0.930202, 0.355409) j_ras = (0.0349643, 0.3597, 0.932413) k_ras = (0.995173, 0.0730758, -0.0655084) writing to /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Mar 5 04:07:23 EST 2018 Found 1 runs /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/rawavg.mgz
/media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018
mri_convert /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/rawavg.mgz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz --conform
mri_convert.bin /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/rawavg.mgz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/rawavg.mgz... TR=9.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0917001, -0.930202, 0.355409) j_ras = (0.0349643, 0.3597, 0.932413) k_ras = (0.995173, 0.0730758, -0.0655084) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz...
mri_add_xform_to_header -c /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/transforms/talairach.xfm /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Mar 5 04:07:32 EST 2018 /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri /usr/local/freesurfer/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 neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux Mon Mar 5 04:07:32 EST 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.1538 /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1538/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1538/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=9.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 7.45058e-09) j_ras = (0, -1.21072e-08, -1) k_ras = (7.45058e-09, 1, 1.16415e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1538/nu0.mnc...
-------------------------------------------------------- Iteration 1 Mon Mar 5 04:07:37 EST 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.1538/nu0.mnc ./tmp.mri_nu_correct.mni.1538/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1538/0/ -iterations 1000 -distance 50 [root@neurodebian:/media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/] [2018-03-05 04:07:37] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1538/0/ ./tmp.mri_nu_correct.mni.1538/nu0.mnc ./tmp.mri_nu_correct.mni.1538/nu1.imp
Processing:.................................................................Done ncvarput: ncid 5: Protocol error miicv_put: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux
recon-all -s 2018 exited with ERRORS at Mon Mar 5 04:07:39 EST 2018
For more details, see the log file /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting