Hi Priti, Thanks for your notice. I thought I disabled dob0, but apparently I didn't... ;-) Now I disabled it and everything works fine!
Best, Martijn On Wed, Feb 22, 2012 at 4:57 PM, Priti Srinivasan < rspr...@nmr.mgh.harvard.edu> wrote: > 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 > > > > 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. > >
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