Well, I was using Freesurfer for some other things, and was thinking that everything would be more consistent if using Freesurfer for all, but perhaps yes, dcm2nii will be the way to go for this instead.
Thanks, pt On Thu, Sep 12, 2013 at 5:18 PM, Harms, Michael <mha...@wustl.edu> wrote: > > The gradient directions, at least as reported in Siemen's DICOMs, are NOT > rotated into the imaging axes. Rather, they are reported in the > coordinate frame of the gradient system. So the conversion tool has to > account for this. Doug will have to comment as to whether mri_convert has > an option to do this. (Why not just use 'dcm2nii'?) > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > > > > On 9/12/13 10:13 AM, "P Taylor" <neon.tay...@gmail.com> wrote: > >>Hi (and thanks for the speedy reply!), >> >> >>There may be some obliquity (from 3dinfo of the created nifti file): >>Data Axes Tilt: Oblique (1.770 deg. from plumb) >> >>I guess if the data were oblique, shouldn't that tilt be included in >>the gradients? Or am I missing something? >> >>And assuming that that information should be included, is there a >>standard way to force that to be included in the mri_convert output? >> >>Thanks very much, >>pt >> >> >> >> >>On Thu, Sep 12, 2013 at 4:50 PM, Harms, Michael <mha...@wustl.edu> wrote: >>> >>> Were these oblique acquisitions? >>> By default, dcm2nii and MRIConvert rotate the bvecs according to the >>> orientation info for oblique acquisitions, whereas it sounds like >>> mri_convert might not be doing that. >>> >>> cheers, >>> -MH >>> >>> -- >>> Michael Harms, Ph.D. >>> >>> ----------------------------------------------------------- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave. Tel: 314-747-6173 >>> St. Louis, MO 63110 Email: mha...@wustl.edu >>> >>> >>> >>> >>> On 9/12/13 9:23 AM, "P Taylor" <neon.tay...@gmail.com> wrote: >>> >>>>Hello, >>>> >>>>I have a question about using mri_convert on diffusion *.dcm files. >>>>When extracted, the gradient table is different than that given by >>>>either MRIConvert (from the UCLA-LCNI webpage) or than dcm2nii of >>>>MRICron; NB: the latter give the *same* results. The differences in >>>>gradient are also not simply sign changes, unfortunately (though, >>>>there is that issue as well, since many x- and y- gradients of >>>>mri_convert are close to the others, but the z-gradient appears to be >>>>uniformly oppositely signed). >>>>This is coupled with the fact that often both the orientation is >>>>different (noted in previous entries), as well as the ORIGIN >>>>information being different. >>>> >>>>Is there any comment about this? And any suggestions about what can >>>>be done to resolve these differences? >>>> >>>>Thanks. >>>>_______________________________________________ >>>>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. >>>> >>> >>> >>> ________________________________ >>> The materials in this message are private and may contain Protected >>>Healthcare Information or other information of a sensitive nature. If >>>you are not the intended recipient, be advised that any unauthorized >>>use, disclosure, copying or the taking of any action in reliance on the >>>contents of this information is strictly prohibited. If you have >>>received this email in error, please immediately notify the sender via >>>telephone or return mail. > > > ________________________________ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
