Hi Gabor, dcm2nii's default setting for VB17 DICOMs should be to rotate the bvecs that it returns into the voxel/image axes if you have a modern version of it.
See item 8 under Sample Datasets of http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html for some notes on this issue and a suggested approach for confirming that your bvecs are correct (albeit in the context of FSL rather than TRACULA, although the two tools are apparently the same in that each expect the bvecs to be in voxel/images axes). cheers, -MH > > Hi Gabor - The input DWIs can be in any format that can be read by > mri_convert, including the NIfTI format. The gradient directions should be > in voxel coordinates, like the ones used by FSL. I don't have experience > with dcm2nii, but if you have original DICOM files, you can pass those as > the input, too. > > Hope this helps, > a.y > > On Thu, 10 May 2012, Gabor Perlaki wrote: > >> Dear all, >> >> Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are >> bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I >> think >> TRACULA needs the bvecs in the image coordinate system, which is not the >> same as scanner coordinate system in case of oblique acquisition. Do I >> need >> to use dcm2nii with correction for slice angulation to >>_______________________________________________ > 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
