Hi Peter - From your dicom header, it looks like the fields that it's looking for to guess which standard Siemens gradient table to use are not there. So you'll have to pass the gradient table and the b-value table as separate text files using bvecfile and bvalfile.
Starting in 6.0 this'll all be more seemless, I promise! a.y On Fri, 5 Feb 2016, Parzer, Peter wrote: > Hi Anastasia, > > no, I did not define "bvecfile" and "bvalfile" in the configuration file, > because the tutorial says, that these variables are not needed if the data is > in Siemens DICOM format, and my data is in Siemens DICOM format. Do I need > this additional step to extract bvec and bval from die DICOM images? And what > is the best way to do it? > > Peter > ________________________________________ > Von: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Anastasia Yendiki > <ayend...@nmr.mgh.harvard.edu> > Gesendet: Donnerstag, 4. Februar 2016 16:29 > An: Freesurfer support list > Betreff: Re: [Freesurfer] tracula preproc complains about missing bvec-file > > Hi Peter - Have you defined "bvecfile" in your configuration file? I > suspect it doesn't know where to find the gradient table. > > a.y > > On Thu, 4 Feb 2016, Parzer, Peter wrote: > >> Hi, >> >> trying to do my first steps with tracula I got stuck early in the >> preprocessing step. The DICOM import and preparation for FSL seem to work >> (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then >> trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does >> not exist. What did I wrong? >> >> The command I used was >> >> trac-all -prep -c dmrirc >> >> The content of the configuration file "dmrirc" was the minimum as described >> in the tutorial: >> >> setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer >> set dtroot = /dat/Hirnreifung/Auswertung/freesurfer >> set subjlist = (3001LT) >> set dcmroot = /dat/Hirnreifung/Daten/DICOM >> set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm) >> >> dcminfo.dat and trac-all.log are in the attachments. >> >> Peter > _______________________________________________ > 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. > > > _______________________________________________ > 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
