Hi Matt,
we made the same experience. Nevertheless, the dcm2nii output differs from the dicom header entries
(and the vectors we put in the sequence) And it does so considerably.
Especially since we often measure angulated.
Before dcm2nii had gave bvecs and bvals, we always used the directions obtained from our physicist.
That also worked fine.
But since they differ, there can only be one correct one. Am I right?
I do not worry about FA, but tracking should be affected.
Thanks for your help,
Mareike
Matt Glasser wrote:
> I have found the dcm2nii output to work very well and not require any manual
> adjustments.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Andreas Bartsch
> Sent: Thursday, May 14, 2009 3:50 AM
> To: [log in to unmask]
> Subject: [FSL] AW: [FSL] bvecs in nifti space of in dicom space?
>
> Hi,
> probably the latter. I guess the former are in magnet (xyz) not patient
> resp. phase-read-slice coordinates (prs). However, you need to figure out
> yourself to be 100% sure. If you have not angulated your acquisition, the
> values should be the same.
> Cheers-
> Andreas
>
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von
> Mareike Menz [[log in to unmask]]
> Gesendet: Donnerstag, 14. Mai 2009 10:14
> An: [log in to unmask]
> Betreff: [FSL] bvecs in nifti space of in dicom space?
>
> Dear FSLers,
>
> we noticed that the bvecs differ in dependence of the readout method.
> An inhouse script reads out the dicom entries as does spm with the helper
> from the diffusion
> toolbox. We already noticed a deviance of these to the gradient table our
> physicist put in but this
> was rather small (maybe due to rounding).
> Now we found out that the dcm2nii output provides yet another gradient
> table. If I understood Chris
> Rorden correctly, this is, because dcm2nii reports the bvecs in NIFTI-space.
>
> Which one should be used for dtifit, and even more important for bedpostx?
>
> Thanks for your answer,
> Mareike
>
> --
> Mareike Menz
> NeuroImage Nord Lübeck
> University Medical Center Hamburg-Eppendorf, Bldg. S10
> Martinistr. 52
> 20246 Hamburg
> Germany
> +49 40 7410 53683
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--
Mareike Menz
NeuroImage Nord Lübeck
University Medical Center Hamburg-Eppendorf, Bldg. S10
Martinistr. 52
20246 Hamburg
Germany
+49 40 7410 53683
[log in to unmask]
-------------------------
() ascii ribbon campaign
/\ - against html mail
--
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
Universitätsklinikum Hamburg-Eppendorf
Körperschaft des öffentlichen Rechts
Gerichtsstand: Hamburg
Vorstandsmitglieder:
Prof. Dr. Jörg F. Debatin (Vorsitzender)
Dr. Alexander Kirstein
Ricarda Klein
Prof. Dr. Dr. Uwe Koch-Gromus
|