[Mrtrix-discussion] CSD

[Luetzkendorf, Ralf]

Hi Donald,

thanks for the quick answer.

1. What I meant with 1. was, if I have one ODF in my image, can I get some values for that ODF, like:
- how many directions it has and how strong
- angle
- vector
or something. So that I have something for a statistics or to compare to subjects in that voxel or the same subject with different measurment parameters or different MR Scanners.

Im not sure if "find_SH_peaks" does that. I will test it.

2. If I open MPRage with MRview and overlay DWI and they have not the same resolution. Does it register the DWI to the MPRage or the MPrage to the DWI?

Thanks for the help and sorry for the inexplicit questions,

Ralf


+++++++++++++++++++++++++++++++++++++++++++++++
Ralf Lützkendorf
Department for Biometry and Medical Informatics
University of Magdeburg, Germany
phone: +49 391 67 13546
fax: +49 391 67 13536

________________________________
Von: Donald Tournier [jdtournier at gmail.com]
Gesendet: Montag, 16. Juni 2014 19:29
An: Lützkendorf, Ralf
Cc: mrtrix mailinglist
Betreff: Re: [Mrtrix-discussion] CSD


Hi Ralf,

I'm assuming you're talking about the stable version of MRtrix (the 0.2.x branch)? If so:

> 1. Is there a way to have a selected ODF in values, angles or something? Would be interesting to see or compare!
>

I'm not sure what you mean by that exactly. You can use find_SH_peaks to get the vectors corresponding to the fODF peaks (scaled by their amplitude), maybe this is what you're after?

> 2. What does MRViewer do if you overlay DWI over anatomie? Is it interpolating the DWI or the Anatomie or something in between?

Both images are interpolated, unless you  explicitly turn it off AND 'lock to image axes' is on (the default), in which case the main image is not interpolated. The overlay image is always interpolated, but if both images align exactly, then the interpolation has negligible effect.

> 3. Is there a way to do the TDI for the Gray matter? I set the thresgold for the FA Map very low, but its not enough I guess!

There is no FA threshold with streamtrack unless you use the DT_STREAM algorithm, which isn't recommended for TDI (actually, it isn't recommended under any circumstances). If you set the cutoff sufficiently low, you should be able to track through these regions, although how good the results are will depend very much on how good your data are, these regions are really noisy at best... So not too sure why you would have trouble with that, unless 'setting the FA threshold' is a different operation from what I think it is... ?

Cheers,
Donald a

>
>
> Thanks for the help,
>
> Ralf
>
>
>
> +++++++++++++++++++++++++++++++++++++++++++++++
> Ralf Lützkendorf
> Department for Biometry and Medical Informatics
> University of Magdeburg, Germany
> phone: +49 391 67 13546
> fax: +49 391 67 13536
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> Mrtrix-discussion mailing list
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