Hi Kate
so something is going wrong with the MNI NU correct tool. Maybe someone on the FS list knows how to fix this, but if not you might want to check with the MNI people
cheers Bruce
On Tue, 14 Oct 2014, Kate Riggall wrote:
Hi Bruce, The output is as follows:
fsuser@xubuntu-VirtualBox:~$ cd /home/fsuser/host/Sprachlernen/Subjects/Y03/mri fsuser@xubuntu-VirtualBox:~/host/Sprachlernen/Subjects/Y03/mri$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /home/fsuser/host/Sprachlernen/Subjects/Y03/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 xubuntu-VirtualBox 3.13.0-37-generic #64-Ubuntu SMP Mon Sep 22 21:30:01 UTC 2014 i686 i686 i686 GNU/Linux Mon Oct 13 18:34:45 EDT 2014 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 tmpdir is ./tmp.mri_nu_correct.mni.2131 /home/fsuser/host/Sprachlernen/Subjects/Y03/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2131/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2131/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=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-08, -5.82077e-08) j_ras = (-1.40164e-07, -4.12911e-10, -1) k_ras = (3.44589e-08, 1, 1.58252e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2131/nu0.mnc...
Iteration 1 Mon Oct 13 18:34:49 EDT 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.2131/nu0.mnc ./tmp.mri_nu_correct.mni.2131/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2131/0/ -iterations 1000 -distance 50 defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [fsuser@xubuntu-VirtualBox:/home/fsuser/host/Sprachlernen/Subjects/Y03/mri/ ] [2014-10-13 18:34:49] 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 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2131/0/ ./tmp.mri_nu_correct.mni.2131/nu0.mnc ./tmp.mri_nu_correct.mni.2131/nu1.imp
Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct
Thanks for your help.
Kate
On Tue, Oct 14, 2014 at 8:29 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Kate
can you run: cd /home/fsuser/host/Sprachlernen/Subjects/Y03/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz and send us the full screen output? thanks Bruce On Tue, 14 Oct 2014, Kate Riggall wrote: Hello, I am using freesurfer for the first time, and I am having issues when I try to run recon-all for my first subject. My details are: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Debian version: jessie/sid Kernel info: Linux 3.13.0-37-generic i686 Subject name: Y03 Command line: fsuser@xubuntu-VirtualBox:~/host/Sprachlernen$ recon-all -all -subjid Y03 Error message: "recon-all exited with ERRORS at Fri Oct 10 02:42:23 EDT 2014" recon-all.log: attached. I am running freesurfer within Virtual Box on a windows host, and my subjects folder is in a shared folder /home/fsuser/host and is called /home/fsuser/host/Sprachlernen/Subjects I first mounted this shared folder by entering sudo mount -t vboxsf Kate /home/fsuser/host and then designated this as my subjects folder by entering export SUBJECTS_DIR=/home/fsuser/host/Sprachlernen/Subjects I then created the subject data directory using recon-all -i Y03_1 -i Y03_2 -subjid Y03 before running recon-all -all. Any assistance would be much appreciated. Kind regards, Kate Riggall
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