[Neuroimaging] [dipy] Import csd model precomputed by mrtrix

Ariel Rokem arokem at gmail.com
Wed May 25 18:24:48 EDT 2016


On Wed, May 25, 2016 at 1:09 PM, Bago <mrbago at gmail.com> wrote:

> Hi Paolo,
>   mrtrix and dipy define the SH basis slightly differently, so the
> precomputed FOD values need to be adjusted if you want to skip the fit step
> and initialize the Fit object directly. IRC we don't currently have the
> code to do that, but it would be something we'd like to incorporate.
>
> Did they change their basis set when they transitioned to mrtrix3? We do
have these functions:

https://github.com/nipy/dipy/blob/master/dipy/reconst/shm.py#L852-L923

That should work with the previous version of mrtrix (mrtrix2?). You can
use these to transform between coefficient sets:

    sf = sh_to_sf(mrtrix_coeffs, sphere, sh_order, basis_type='mrtrix')
    dipy_coeffs = sf_to_sh(sf, sphere, sh_order, basis_type=None) # This
defaults to the dipy basis set

and then use the CSD model object to predict:

    from dipy.reconst.csdeconv import  ConstrainedSphericalDeconvModel
    csd_model = ConstrainedSphericalDeconvModel(gtab, response,
sh_order=sh_order) # Note: you still need to calculate the response
function!
    pred_signal = csd_model.predict(dipy_coeffs, gtab, S0)

I think that something like this should work (but I haven't tried it
myself).


> I have a WIP version of the multi-shell CSD model on a separate branch, I
> plan on merging it but wasn't intending to get to that for a few months. If
> you'd like to look at before then I can push the branch up to github.
>
> Sounds interesting! I'd love to see what you have so far!

Cheers,

Ariel


> Bago
>
> On Wed, May 25, 2016 at 2:31 AM Paolo Avesani <avesani at fbk.eu> wrote:
>
>> I would like to take advantage of the "predict" method of reconstruction
>> models in dipy. The goal is to assess the quality of results.
>>
>> I have already computed the reconstruction models using mrtrix3 and
>> stored the ODF files. For this reason I would need to initialize the csd
>> model by importing the data from ODF stored by mrtrix3.
>>
>> The questions are manifold:
>> - may I initialize the csd model by providing the precomputed values and
>> skipping the "fit" step?
>> - may I import the value of precomputed model from a file stored by
>> mrtrix3?
>> - is the csd model in dipy compliant with the output of multi-shell csd
>> model computed by mrtrix3?
>>
>> I hope my questions and my goal is formulated clearly.
>> Thanks for your support.
>> Paolo
>>
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