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 < rspriti@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
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