Dear all,
I'm trying to run trac-all (FS5.1, the updated trac-all) for a provided nii.gz DWI volume and it's bvals/bvecs. During the preprocessing mri_convert searches for dti/COR-.info, but cannot find it - see log below. Does anyone have a clue why it searches for this COR-.info file?
Best, Martijn
#------------------------------------- /usr/local/freesurfer51/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Feb 22 13:45:42 CET 2012 mri_convert /haso/msteenwj/test_data/V3T/dti/raw.nii.gz /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz mri_convert /haso/msteenwj/test_data/V3T/dti/raw.nii.gz /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /haso/msteenwj/test_data/V3T/dti/raw.nii.gz... TR=13000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.994366, -0.0972332, -0.0422076) j_ras = (-0.0971699, 0.995259, -0.00408943) k_ras = (-0.0424052, -3.49181e-05, 0.999101) writing to /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz... cp /haso/msteenwj/test_data/V3T/dti/bvecs_old /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvecs cp /haso/msteenwj/test_data/V3T/dti/bvals /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvals flip4fsl /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -2.39997 fslswapdim /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz x y z /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.nii.gz INFO: found /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.mghdti.bvecs /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/bvecs mv -f /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.mghdti.bvals /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/bvals mri_convert /haso/msteenwj/test_data/V3T/dti/ /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/b0mag.nii.gz mri_convert /haso/msteenwj/test_data/V3T/dti/ /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/b0mag.nii.gz corRead(): can't open file /haso/msteenwj/test_data/V3T/dti/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /haso/msteenwj/test_data/V3T/dti/... Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Feb 22 13:52:47 CET 2012