[Mrtrix-discussion] 2 NEX

[Robert Smith]

Romain

The issue here is that estimate_response automatically determines the
maximum harmonic order lmax based on the number of diffusion-weighted
directions it finds in the DWI. In the case of your data, it finds 60
diffusion-weighted directions, so fits a spherical harmonic order of 8
(which requires 45 coefficients). However you only actually have 30 unique
directions, with each acquired twice. So there is only enough angular
resolution to fit a spherical harmonic order of 6 (which requires 28
coefficients). If you provide the option -lmax 6 to estimate_response, it
calculates a response function similar to those you obtained from each
half-dataset.

CSD is capable of calculating Fibre Orientation Distributions of a higher
order than you have the data to support ('super-resolved' CSD), as it
incorporates additional information from those directions where the FOD is
negative. You _may_ be able to perform CSD with an lmax of 8, but it is
possible that some voxels will fail to converge (this will give an error on
the command-line, and the corresponding voxel in your image will be black
and contain NAN values). If this occurs frequently in your images, you will
be limited to using an lmax of 6 for CSD for these data (use "-lmax 6" at
the command line for csdeconv).

Best regards
Rob


--

Robert Smith
PhD Candidate

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7128
Fax: +61 3 9035 7301
www.florey.edu.au



On Wed, Dec 5, 2012 at 2:41 AM, romain valabregue <romain.valabregue at upmc.fr
> wrote:

> Dear All
>
> I have an acquisition which has been done with the same direction twice.
> (this was an error intead of using a complementary set of direction it uses
> the same diffusion directions)
>
> when I do the estimate_response on the all data set I get wrong estimation
>
>  cat response.txt
> -4.04413e+15 1.47696e+14 -1.52359e+15 -3.50894e+15 6.85026e+15
>
>
> but when I do the estimation on the half of the dataset (either the first
> one or the second one)
> I get a correct estimation
>
> cat response_sh.txt
> 504.145 -226.698 65.6188 -14.786
> cat response_sh2.txt
> 492.199 -215.285 64.4914 -10.5965
>
>
> Any idea how I can handle the 2 NEX correctly in mrtrix
>
>
> Thanks
>
>
> Romain
>
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