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. > > [EMAIL PROTECTED] 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... > #-------------------------------------------- > [EMAIL PROTECTED] 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 > #-------------------------------------------- > [EMAIL PROTECTED] 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 [EMAIL PROTECTED] (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 > [EMAIL PROTECTED]:/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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
