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

[Bago]

Samuel mrtrix has at least two models implemented. The multi-shell
(multi-tissue) model cannot be used with single shell data and the original
CSD model cannot be used with multi-shell data.

Bago

On Wed, May 25, 2016 at 5:13 PM Samuel St-Jean <stjeansam at gmail.com> wrote:

> Their wiki explains it, a sqrt(2) to normalize is used in mrtrix3, so
> multiplying your coefficients with that and using the mrtrix2 functions
> should do it.
>
> Although dipy only does single shell, so conclude with consideration that
> the algorithm is different from mrtrix3. Also, csd is a bad signal
> predictor (but good for angle estimation), see the sparc dmri challenge
> paper for example.
> On May 26, 2016 07:55, "Ariel Rokem" <arokem at gmail.com> wrote:
>
>>
>>
>> On Wed, May 25, 2016 at 4:41 PM, Bago <mrbago at gmail.com> wrote:
>>
>>> I believe they did change their basis (please correct me if I'm wrong
>>> but I believe they went from a non-normalized SH basis to a normalized SH
>>> basis).
>>>
>>>
>> So they have the same basis as dipy now, but the coefficients appear in a
>> different order? That should make life even easier!
>>
>>
>>> Also projecting onto a sphere is one way to _estimate_ the coefficients
>>> in a different basis. The cleaner way is to just re-order the coefficients
>>> and apply the appropriate scaling. If both basis are normalized (which dipy
>>> is) the scaling should be 1 or -1.
>>>
>>>
>> Fair point, but to be just a little bit facetious: given enough points on
>> the sphere and knowledge of the target maximal order of the coefficients,
>> wouldn't estimating be the same as transforming? Works for the FFT, I
>> believe :-)
>>
>> Bago
>>>
>>> On Wed, May 25, 2016 at 3:31 PM Ariel Rokem <arokem at gmail.com> wrote:
>>>
>>>> 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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