Bruce, Thanks for your help. I will forward this to the MNI mailing list and see if they can help.
Cheers, Kate On Tue, Oct 14, 2014 at 10:46 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > 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 <fis...@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 >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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