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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