Hi All,<br><br>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&#39;t get it to work. Any help is appreciated. <br><br>Thanks,<br>
<br>Anil.<br><br>[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<br>INFO: SUBJECTS_DIR is /mnt/win/MRI_data/MWIN4/Freesurfer<br>
Actual FREESURFER_HOME /usr/local/freesurfer<br>Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux<br>WM removal version<br>/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002<br>&nbsp;<br>&nbsp;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<br>&nbsp;<br>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
<br>reading from /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-0002-0001-0001.dcm...<br>Getting Series No<br>INFO: Found 162 files in /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom<br>INFO: Scanning for Series Number 2
<br>Scanning Directory<br>INFO: found 160 files in series<br>INFO: loading series header info.<br>&nbsp;<br>RunNo = 1<br>INFO: sorting.<br>INFO: (192 256 160), nframes = 1, ismosaic=0<br>FileName&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-
0002-0001-0001.dcm<br>Identification<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; NumarisVer&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; syngo MR 2006T 4VB12T<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ScannerModel&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; TrioTim<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PatientName&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9702<br>Date and time<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; StudyDate&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 20070328<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; StudyTime&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
113239.765000<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SeriesTime&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 114403.109000<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; AcqTime&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 113640.352512<br>Acquisition parameters<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PulseSeq&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; tfl3d1<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Protocol&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; MPRAGE AXIAL<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PhEncDir&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ROW
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EchoNo&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; FlipAngle&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; EchoTime&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.36<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; InversionTime&nbsp;&nbsp;&nbsp;&nbsp; 900<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; RepetitionTime&nbsp;&nbsp;&nbsp; 2300<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PhEncFOV&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 192<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ReadoutFOV&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 256
<br>Image information<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; RunNo&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SeriesNo&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ImageNo&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; NImageRows&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 256<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; NImageCols&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 192<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; NFrames&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SliceArraylSize&nbsp;&nbsp; 1
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; IsMosaic&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ImgPos&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 101.4164 183.6733 -63.6460<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; VolRes&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.0000&nbsp;&nbsp; 1.0000&nbsp;&nbsp; 1.0000<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; VolDim&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 192 256 160<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Vc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.9991
&nbsp;&nbsp; 0.0030&nbsp; -0.0434<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Vr&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.0000&nbsp; -0.9977&nbsp; -0.0681<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Vs&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.0435&nbsp; -0.0680&nbsp;&nbsp; 0.9967<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; VolCenter&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.0258&nbsp; 50.8135&nbsp;&nbsp; 3.2105<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; TransferSyntaxUID 1.2.840.10008.1.2.1
<br>INFO: no Siemens slice order reversal detected (good!).<br>TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00<br>i_ras = (-0.999053, 0.00296272, -0.0434174)<br>j_ras = (-2.12178e-10, -0.99768, -0.0680798)<br>k_ras = (-0.0435184
, -0.0680153, 0.996735)<br>writing to /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz...<br>#--------------------------------------------<br>#@# MotionCor Sun Nov&nbsp; 4 16:38:15 CST 2007<br>Found 1 runs<br>/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz
<br>WARNING: only one run found. This is OK, but motion<br>correction cannot be performed on one run, so I&#39;ll<br>copy the run to rawavg and continue.<br>&nbsp;<br>&nbsp;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
<br>&nbsp;<br>/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002<br>&nbsp;<br>&nbsp;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<br>&nbsp;<br>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
<br>reading from /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz...<br>TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00<br>i_ras = (-0.999053, 0.00296272, -0.0434174)<br>j_ras = (-2.12178e-10, -0.99768, -0.0680798
)<br>k_ras = (-0.0435184, -0.0680153, 0.996735)<br>Original Data has (1, 1, 1) mm size and (192, 256, 160) voxels.<br>Data is conformed to 1 mm size and 256 voxels for all directions<br>changing data type from 4 to 0 (noscale = 0)...
<br>MRIchangeType: Building histogram<br>Reslicing using trilinear interpolation<br>writing to /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz...<br>&nbsp;<br>&nbsp;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
<br>&nbsp;<br>INFO: extension is mgz<br>#--------------------------------------------<br>#@# Nu Intensity Correction Sun Nov&nbsp; 4 16:38:45 CST 2007<br>&nbsp;<br>&nbsp;mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2<br>&nbsp;<br>/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri
<br>/usr/local/freesurfer/bin//mri_nu_correct.mni<br>--i orig.mgz --o nu.mgz --n 2<br>nIters 2<br>$Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $<br>Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux
<br>Sun Nov&nbsp; 4 16:38:45 CST 2007<br>Program nu_correct, built from:<br>Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27<br>tmpdir is ./tmp.mri_nu_correct.mni.7437<br>/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri
<br>mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7437/nu0.mnc<br>mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7437/nu0.mnc<br>Can&#39;t find the talairach xform &#39;/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm&#39;
<br>Transform is not loaded into mri<br>reading from orig.mgz...<br>&nbsp; Talairach transform /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm does not exist ...<br>Cannot load tal xfm file /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm
<br>TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00<br>i_ras = (-1, -1.52311e-10, -6.04436e-10)<br>j_ras = (5.26148e-10, 2.33896e-09, -1)<br>k_ras = (1.65039e-10, 1, 5.09647e-09)<br>writing to ./tmp.mri_nu_correct.mni.7437/nu0.mnc...
<br>Outputting Volume: ............................................................<br>&nbsp; <br>--------------------------------------------------------<br>Iteration 1 Sun Nov&nbsp; 4 16:39:03 CST 2007<br>nu_correct -clobber ./tmp.mri_nu_correct.mni.7437/nu0.mnc ./tmp.mri_nu_correct.mni.7437/nu1.mnc
<br>[root@wonglinux1:/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/] [2007-11-04 16:39:03] running:<br>&nbsp; /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
<br>&nbsp;<br>Assertion failed at line 827 in file templates/CachedArray.cc<br>nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)<br>nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
<br>ERROR: nu_correct<br>Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux<br>&nbsp;<br>recon-all exited with ERRORS at Sun Nov&nbsp; 4 16:39:07 CST 2007<br>