This seems to be occurring for all subjects including subjects from different experiments. I should mention here that I'm running this data from another machine (input of dicom files and data output from Freesurfer). The local machine ran out of space so I decided to use this alternative.

I don't think there is an MNI installation in the path apart from the MNI tools provided by Freesurfer. Here is the output of echo $PATH

[root@wonglinux1 freesurfer]# echo $PATH
/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/bin/noarch:/usr/local/freesurfer/bin/:/usr/local/freesurfer/fsl/bin:/usr/local/freesurfer/lib/tcltktixblt/bin:/usr/local/freesurfer/lib/gsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/root/abin:/usr/local/fiswidgets- 2.3:/usr/X11R6/bin:/root/bin:/root/abin:/usr/local/fiswidgets-2.3:/root/bin:/root/abin:/usr/local/fiswidgets-2.3

Thanks,

Anil.

On Nov 4, 2007 6:35 PM, Nick Schmansky < nicks@nmr.mgh.harvard.edu> wrote:
Anil,

Does this occur for just this subject?  Or all subjects?  Is it
repeatable?  Is there another MNI installation somewhere in the path?

Nick


On Sun, 2007-11-04 at 15:51 -0600, Anil Roy wrote:
> Hi All,
>
> I got the following error while running recon-all on a set of dicoms.
> It seems to be a problem with the intensity correction stage but I
> can't get it to work. Any help is appreciated.
>
> Thanks,
>
> Anil.
>
> [root@wonglinux1 freesurfer]# recon-all -
> i /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-0002-0001-0001.dcm -s O-07-002 -autorecon-all
> INFO: SUBJECTS_DIR is /mnt/win/MRI_data/MWIN4/Freesurfer
> Actual FREESURFER_HOME /usr/local/freesurfer
> Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686
> i386 GNU/Linux
> WM removal version
> /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002
>
>  mri_convert /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-
> 0002-0001-0001.dcm /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz
>
> mri_convert /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-0002-0001-0001.dcm /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz
> reading
> from /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-0002-0001-0001.dcm...
> Getting Series No
> INFO: Found 162 files
> in /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom
> INFO: Scanning for Series Number 2
> Scanning Directory
> INFO: found 160 files in series
> INFO: loading series header info.
>
> RunNo = 1
> INFO: sorting.
> INFO: (192 256 160), nframes = 1, ismosaic=0
> FileName                /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702- 0002-0001-0001.dcm
> Identification
>         NumarisVer        syngo MR 2006T 4VB12T
>         ScannerModel      TrioTim
>         PatientName       9702
> Date and time
>         StudyDate         20070328
>         StudyTime         113239.765000
>         SeriesTime        114403.109000
>         AcqTime           113640.352512
> Acquisition parameters
>         PulseSeq          tfl3d1
>         Protocol          MPRAGE AXIAL
>         PhEncDir          ROW
>         EchoNo            0
>         FlipAngle         9
>         EchoTime          3.36
>         InversionTime     900
>         RepetitionTime    2300
>         PhEncFOV          192
>         ReadoutFOV        256
> Image information
>         RunNo             1
>         SeriesNo          2
>         ImageNo           1
>         NImageRows        256
>         NImageCols        192
>         NFrames           1
>         SliceArraylSize   1
>         IsMosaic          0
>         ImgPos            101.4164 183.6733 -63.6460
>         VolRes              1.0000   1.0000   1.0000
>         VolDim            192 256 160
>         Vc                 - 0.9991    0.0030  -0.0434
>         Vr                 -0.0000  -0.9977  -0.0681
>         Vs                 -0.0435  -0.0680   0.9967
>         VolCenter           2.0258  50.8135   3.2105
>         TransferSyntaxUID 1.2.840.10008.1.2.1
> INFO: no Siemens slice order reversal detected (good!).
> TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00
> i_ras = (-0.999053, 0.00296272, -0.0434174)
> j_ras = (-2.12178e-10 , -0.99768, -0.0680798)
> k_ras = (-0.0435184 , -0.0680153, 0.996735)
> writing
> to /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz...
> #--------------------------------------------
> #@# MotionCor Sun Nov  4 16:38:15 CST 2007
> Found 1 runs
> /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz
> 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 /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz
>
> /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002
>
>  mri_convert /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz --conform
>
> mri_convert /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz --conform
> reading
> from /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz...
> TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00
> i_ras = (-0.999053, 0.00296272, -0.0434174)
> j_ras = (-2.12178e-10 , -0.99768, -0.0680798 )
> k_ras = (-0.0435184, -0.0680153, 0.996735)
> Original Data has (1, 1, 1) mm size and (192, 256, 160) voxels.
> Data is conformed to 1 mm size and 256 voxels for all directions
> changing data type from 4 to 0 (noscale = 0)...
> MRIchangeType: Building histogram
> Reslicing using trilinear interpolation
> writing to /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz...
>
>  mri_add_xform_to_header -
> c /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz
>
> INFO: extension is mgz
> #--------------------------------------------
> #@# Nu Intensity Correction Sun Nov  4 16:38:45 CST 2007
>
>  mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
>
> /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri
> /usr/local/freesurfer/bin//mri_nu_correct.mni
> --i orig.mgz --o nu.mgz --n 2
> nIters 2
> $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $
> Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686
> i386 GNU/Linux
> Sun Nov  4 16:38:45 CST 2007
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-
> gnu) on 2005-11-15 at 21:02:27
> tmpdir is ./tmp.mri_nu_correct.mni.7437
> /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7437/nu0.mnc
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7437/nu0.mnc
> Can't find the talairach xform
> '/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm'
> Transform is not loaded into mri
> reading from orig.mgz...
>   Talairach
> transform /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm does not exist ...
> Cannot load tal xfm
> file /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm
> TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00
> i_ras = (-1, -1.52311e-10, -6.04436e-10)
> j_ras = (5.26148e-10, 2.33896e-09, -1)
> k_ras = (1.65039e-10, 1, 5.09647e-09)
> writing to ./tmp.mri_nu_correct.mni.7437/nu0.mnc...
> Outputting
> Volume: ............................................................
>
> --------------------------------------------------------
> Iteration 1 Sun Nov  4 16:39:03 CST 2007
> nu_correct -
> clobber ./tmp.mri_nu_correct.mni.7437/nu0.mnc ./tmp.mri_nu_correct.mni.7437/nu1.mnc
> [root@wonglinux1:/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/]
> [2007-11-04 16:39:03] running:
>   /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -
> sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -
> nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp
> -
> tmpdir /usr/tmp/nu_correct_7482/ ./tmp.mri_nu_correct.mni.7437/nu0.mnc ./tmp.mri_nu_correct.mni.7437/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
> Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686
> i386 GNU/Linux
>
> recon-all exited with ERRORS at Sun Nov  4 16:39:07 CST 2007
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer