Hi Matt, Thanks a lot for the clarification.
Best, Szabolcs On Fri, Aug 11, 2017 at 2:32 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > It looks like you have the correct understanding of this. One cannot > easily apply the gradient nonlinearity effects on the diffusion gradients > to the images, as really you need to apply them to the bvals and bvecs. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Szabolcs David > <davidszabolc...@gmail.com> > Date: Thursday, August 10, 2017 at 7:03 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] DTI on HCP data > > Dear HCP Team, > > I would like to use HCP diffusion data to do some diffusion tensor fitting > and subsequently calculate maps of FA, MD, etc. For this I think it would > be handy to use the followings: > $subject\T1w\Diffusion\bvals > $subject\T1w\Diffusion\bvecs > $subject\T1w\Diffusion\data.nii.gz > > We can refer to these files as the result of the 'minimal processing > pipeline' (Glasser 13 Neuroimage), as this diffusion data is already > processed for motion and B0 inhomogeneities among many other artifacts. But > since I would like to do some custom-made model estimation (aka. outside of > FSL/dtifit/bedpostx), I need to implement a voxelwise bvecs rotation and > bval calculation, because of the effect of the diffusion gradient > nonlinearities. To do this the source is the > $subject\T1w\Diffusion\grad_dev.nii.gz > file. > A bit of matlab script is provided to calculate the proper bvec and bval > per voxel. (this guy: http://www.humanconnectome.org/storage/ > app/media/documentation/data_release/Q1_Release_Appendix_II.pdf). > > Generally: I am right with the above? In the mentioned paper this part is > a bit confusing for me (highlighted some parts): > > "The gradient nonlinearity correction warpfield is then calculated for > the diffusion data to remove this spatial distortion (Jovicich et al., > 2006), and the mean b0 image is distortion corrected. *Additionally, the > effects of gradient nonlinearity on the diffusion encoding magnitudes and > directions are calculated (Bammer et al., 2003; Sotiropoulos it et al., > 2013–this issue).* The partial derivatives of the spatially-dependent > magnetic field are used to calculate a gradient field tensor at each voxel, > which maps “nominal” to actual gradient magnitudes and directions (Bammer > et al., 2003). *Using the gradient field tensor, the magnitude and > direction of the diffusion-sensitizing gradients can be corrected at each > brain voxel.* This information is subsequently used for more accurate > fiber orientation estimation." > > In short: the diffusion weighted gradient nonlinearities are calculated, > BUT not applied. That is why every time one wants to do model estimation > diffusion gradient nonlinearities must be considered in a form to use > different bvals and bvecs per voxel. In FSL for dtifit that would be > calling the --gradnonlin option. In contrast, distortions from (regular) > imaging gradients are corrected, after topup+eddy based correction for B0 > inhomogeneities and eddy current distortion correction. This is stated > right after the cited paragraph from the same paper: > "It is worth noting that the gradient nonlinearity correction is done at a > much later stage in the diffusion pipeline than in the fMRIVolume pipeline.* > Ideally the gradient nonlinearity distortion correction would be done > simultaneously with the B0 inhomogeneity distortion correction, as well as > with the eddy current distortion correction and rigid-body motion > correction, as all of these interact*." -> but here the "gradient > nonlinearity distortion correction" is about the imaging gradients, right? > The correction of diffusion gradient nonlinearities are *still* stored in > the grad_dev.nii.gz file and must be used during model estimation. > > Apologies for the long email. > > Best, > Szabolcs > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
