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
