[Mrtrix-discussion] Tensors in mrview

[René Besseling]

Yep, that's the references I meant. And I found my script, but it's not
suitable for stand-alone redistribution. However, it's quite simple and I
didn't even use the analytical expression; I simply calculated b g' D g for
every voxel and fitted this to SHs up to order 2. I used Donald's m-file
gen_scheme to construct the SH basis. When writing the SHs to nii to load
into MRtrix, indeed keep in mind to mutiple the m=~0 components by sqrt(2)

René
On Sun, Oct 28, 2012 at 11:23 AM, Thijs Dhollander <
thijs.dhollander at uzleuven.be> wrote:

>  Hello everyone,****
>
> ** **
>
> The analytic expression to convert forth and back between SH coefficients
> and tensor parameters has been described in this paper from Descoteaux et
> al. (2006):****
>
> ** **
>
> http://onlinelibrary.wiley.com/doi/10.1002/mrm.20948/full ****
>
> ** **
>
> …more specifically, matrix M in equation 17, of which the solution for the
> rank-2 tensor and SH basis up to order 2 is shown in figure 3.  Be careful
> however, as this assumes the orthornomal SH basis that Maxime Descoteaux
> defined in that paper in equation 11 (and typically used in most of his
> following works).  The SH basis used in MRtrix is slightly different; a
> description of it can be found at e.g.****
>
> ** **
>
> http://www.brain.org.au/software/mrtrix/commands/dwi2SH.html ****
>
> ** **
>
> The differences are the omission of the conventional (-1)^m factor, as
> well as an additional factor sqrt(2) for the Y(l,m) coefficients where m is
> not 0.****
>
> ** **
>
> Cheers,****
>
> Thijs****
>
> ** **
>
> *Thijs Dhollander*
> PhD Student
>
> thijs.dhollander at uz.kuleuven.ac.be
> tel. +32 16 34 90 37
> gsm. +32 475 36 44 27*
>
> **Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)
> *Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus
> 7003 | B-3000 Leuven | http://www.medicalimagingcenter.be****
>
> ** **
>
> *From:* mrtrix-discussion-bounces at public.nitrc.org [mailto:
> mrtrix-discussion-bounces at public.nitrc.org] *On Behalf Of *René Besseling
> *Sent:* Saturday, October 27, 2012 11:31
> *To:* Ariel Rokem
> *Cc:* Arnaud Boré; mrtrix-discussion at public.nitrc.org
> *Subject:* Re: [Mrtrix-discussion] Tensors in mrview****
>
> ** **
>
> There is this analytical expression to express g'Dg in spherical
> harmonics, but it'quite a while back that I looked into that. I'll check in
> on monday on my pc at work.****
>
>  ****
>
> René****
>
> On Sat, Oct 27, 2012 at 1:47 AM, Ariel Rokem <arokem at gmail.com> wrote:****
>
> Hi Rene, ****
>
> ** **
>
> I would actually like to see that. Is there an analytic expression for
> that, or do you perform some kind of approximation? Could you put the code
> somewhere (e.g. gist.github.com)? ****
>
> ** **
>
> Thanks, ****
>
> ** **
>
> Ariel ****
>
> ** **
>
> On Fri, Oct 26, 2012 at 3:41 PM, René Besseling <r.m.h.besseling at gmail.com>
> wrote:****
>
> Jep, you can express their peanut-shaped representation (so not the
> ellipsoid) in spherical harmonics. If you're interested, I've got a Matlab
> script that takes the dt.nii from dwi2tensor as an input at outputs the SH
> representation.****
>
>  ****
>
> René****
>
> On Fri, Oct 26, 2012 at 8:10 PM, Arnaud Boré <arnaud.bore at gmail.com>
> wrote:****
>
>   Hello MRtrix users,****
>
> ** **
>
> Just want to know if there is a way to see tensors in mrview.****
>
> ** **
>
> Thanks****
>
> Arnaud****
>
> ** **
>
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