Hi Martin, Are you including b0 correction in your preprocessing stream? I can see b0mag.nii.gz in your log file.
Did you set dob0 = 1 in your configuration file? If so you have to set also the magnitude and phase maps (using set b0mlist and set b0plist in the configuration file,Check out $FREESURFER_HOME/bin/dmrirc.example for more details on how to set up the configuration file for using b0 correction in your stream). Can you check if you've set that correctly? If you've accidentally included set dob0 = 1, but do not want to do b0 correction, you can comment out or remove that line from your configuration file and re-run trac-all -prep again. If you can check that and let us know for starters, we can figure out what is going on. Hope this is helpful, Priti mri_convert /haso/msteenwj/test_data/V3T/dti/ /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/b0mag.nii.gz > 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 > _______________________________________________ > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
