[Freesurfer] recon-all error

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