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

Wed May 25 22:07:29 EDT 2016

Indeed, I thought I read the multitissue version was used here, my mistake
as the question does not directly imply that.

The regular single shell hopefully does the same (at least I can personally
attest the mrtrix2 version and dipy version give similar fodf up to a small
rounding factor, but that was before the cholesky decomposition step, so
now they should behave the same).
On May 26, 2016 09:37, "Bago" <mrbago at gmail.com> wrote:

> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Neuroimaging mailing list
>>>>>>> Neuroimaging at python.org
>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Neuroimaging mailing list
>>>>>> Neuroimaging at python.org
>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>
>>>>>> _______________________________________________
>>>>> Neuroimaging mailing list
>>>>> Neuroimaging at python.org
>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>
>>>>
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/neuroimaging/attachments/20160526/35ae3eea/attachment-0001.html>