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Improve NODDI step in the pipeline #14

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ebrahimebrahim opened this issue Mar 6, 2024 · 1 comment · May be fixed by #20
Open

Improve NODDI step in the pipeline #14

ebrahimebrahim opened this issue Mar 6, 2024 · 1 comment · May be fixed by #20
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@ebrahimebrahim

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@ebrahimebrahim
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  • The current NODDI step using dmipy is too slow
  • It should be possible to choose between Watson and Bingham NODDI

The NODDI step in the pipeline is currently using the dmipy implementation, but it's super slow and can take hours to handle just one image. We should try something else. There's MDT, which has gpu accelerated NODDI estimation, and also AMICO. We should look into both of these.
@ebrahimebrahim
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I just saw to a DIPY workshop talk by Gary Zhang where he recommended using either AMICO or some type of machine learning to quickly get close to the true value, and then from there to use conventional fitting to refine the result.

@ebrahimebrahim ebrahimebrahim self-assigned this Apr 2, 2024
@ebrahimebrahim ebrahimebrahim linked a pull request Apr 2, 2024 that will close this issue
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@ebrahimebrahim ebrahimebrahim linked a pull request Apr 2, 2024 that will close this issue
add AMICO noddi fitting step #20
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@ebrahimebrahim ebrahimebrahim moved this to Will go to Q2 in ABCD Y2Q1 Aug 12, 2024
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Status: Will go to Q2
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add AMICO noddi fitting step brain-microstructure-exploration-tools/abcd-noddi-tbss-experiments
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@ebrahimebrahim @jamesfishbaugh