[Mrtrix-discussion] 2 NEX

[romain valabregue]

Hi

thanks for this clear answer.

I guess then that a possible improvement would be for the 
estimate_response (and csdevonc) programs
to change

-lmax order   set the maximum harmonic order to be estimated. By 
default, the
                 program will use the highest possible lmax given the 
number of
                 diffusion-weighted images.

by


-lmax order   set the maximum harmonic order to be estimated. By 
default, the
                 program will use the highest possible lmax given the 
number of
_/independant direction/__._

Best

Romain

Le 07/12/2012 02:47, Robert Smith a écrit :
> 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 <http://www.florey.edu.au>
>
>
>
> On Wed, Dec 5, 2012 at 2:41 AM, romain valabregue 
> <romain.valabregue at upmc.fr <mailto: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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