Devin,

The VirtualBox install of freesurfer is an unsupported version that has been provided as a convenience to Windows users or other users that wish to use the freesurfer software but do not have immediate access to Mac or Linux platform. The Virtual box installation is literally just an Xubuntu (Linux) disk image with the freesurfer centOS4 build installed on top of it.

That said, if you upload your data I will attempt to recreate the issue you are experiencing. I can not promise a solution will be found but if something obvious jumps out at me I will provide the best advice I can on how to resolve the matter.

-Zeke

On 11/15/2013 05:02 PM, Devin Sodums wrote:

Dear Freesurfer experts,

I have recently installed Freesurfer onto a VirtualBox Linux environment, and had no problems running the supplied practice subject, 'Bert', all the way through reconstruction. However, when I started trying to analyze my own subject's, recon-all keeps exiting just after the "mri_nu_correct.mni" step, without any specific error message. I have copied and pasted the error message from the unsuccessful, and successful run below, as well as the output from the "bugr" command. I realize that tcsh is out of date, and I have tried updating it (which I am not sure if I was successful or not), but I got the same message with the successful run so I don't think that is the issue. Any suggestions would be greatly appreciated.

Best, Devin

General info:

fsuser@xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/b_s_20131018_124417$ which freesurfer

/usr/local/freesurfer/bin/freesurfer

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

Debian version: wheezy/sid

Kernel info: Linux 3.2.0-56-generic i686

**

*Unsuccessful Run:*

xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/boucher_suzanne_20131018_12 4417> recon-all -subjid b_s_20131018_fs -all

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417

Actual FREESURFER_HOME /usr/local/freesurfer

Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux

#--------------------------------------------

#@# MotionCor Fri Nov 15 16:30:12 EST 2013

Found 1 runs

/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/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 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz

/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs

mri_convert /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz --conform

mri_convert /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz --conform

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0.0156845, -0.970744, 0.239606)

j_ras = (0.0185749, 0.239877, 0.970626)

k_ras = (0.999704, 0.0107731, -0.0217938)

Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels.

Data is conformed to 1 mm size and 256 voxels for all directions

changing data type from float to uchar (noscale = 0)...

MRIchangeType: Building histogram

Reslicing using trilinear interpolation

writing to /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz...

mri_add_xform_to_header -c /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/transforms/talairach.xfm /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz

INFO: extension is mgz

#--------------------------------------------

#@# Talairach Fri Nov 15 16:30:45 EST 2013

/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux

recon-all -s b_s_20131018_fs exited with ERRORS at Fri Nov 15 16:30:58 EST 2013

*SUCCESSFUL RUN:*

**

INFO: extension is mgz

#--------------------------------------------

#@# Talairach Fri Nov 15 15:53:35 EST 2013

/usr/local/freesurfer/subjects/bert/mri

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm

INFO: transforms/talairach.xfm already exists!

The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm

This is done to retain any edits made to transforms/talairach.xfm

Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm

#--------------------------------------------

#@# Talairach Failure Detection Fri Nov 15 15:55:03 EST 2013

/usr/local/freesurfer/subjects/bert/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7614, pval=0.6675 >= threshold=0.0050)

awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/bert/mri/transforms/talairach_avi.log

tal_QC_AZS /usr/local/freesurfer/subjects/bert/mri/transforms/talairach_avi.log

TalAviQA: 0.97409

z-score: 0

#--------------------------------------------

#@# Nu Intensity Correction Fri Nov 15 15:55:03 EST 2013

mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2

/usr/local/freesurfer/subjects/bert/mri

/usr/local/freesurfer/bin/mri_nu_correct.mni

--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2

nIters 2

$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $

Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux

Fri Nov 15 15:55:03 EST 2013

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.10351

/usr/local/freesurfer/subjects/bert/mri

mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10351/nu0.mnc -odt float

mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10351/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, 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.10351/nu0.mnc...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer