[Neuroimaging] CZI grant - what would you like to see in Nibabel?

[Matthew Brett]

Hi,

Emanuele - would you mind opening an issue for this?

Can anyone volunteer to lead the new streamlines format group?  I'm
not an expert at all.

Cheers,

Matthew

On Thu, Jul 30, 2020 at 5:03 PM Emanuele Olivetti <olivetti at fbk.eu> wrote:
>
> Hi Matthew,
>
> My colleagues and I would like to have a (much) faster loader of tractography data with a smaller memory footprint, especially for TRK (Trackvis) files. Just to give you an idea - which, yes, it's an extreme case but definitely not so infrequent for us - when loading a very large tractogram of 10 million streamlines it takes:
> - 15 minutes and approximately 10Gb of RAM with Nibabel
> - 1 minute and approximately 5Gb of RAM with our custom TRK loader (it works but code style is meh, https://github.com/FBK-NILab/nilab/blob/master/load_trk.py)
> - 6 seconds and 3.5Gb of RAM if we previously save the tractogram as numpy array (numpy.savez()) and then load it with numpy.load(). But in this case, the streamlines are resampled to a fixed number of points.
>
> Thank you for all the work done!
>
> Emanuele
>
>
> On Thu, Jul 30, 2020 at 5:01 PM Matthew Brett <matthew.brett at gmail.com> wrote:
>>
>> Hi,
>>
>> Although this is pushing things close the wire, I am currently trying
>> to work out whether to apply for a Chan Zuckerberg grant for Nibabel:
>>
>> https://chanzuckerberg.com/wp-content/uploads/2020/06/EOSS-3-RFA-Announcement-and-Instructions-CYCLE-3-COMBINED-1.pdf
>>
>> Before we do that, I wanted to ask - if y'all could get anything into
>> Nibabel - what
>> would it be?
>>
>> So far, in various conversations, Chris Markiewicz and I came up with:
>>
>> * More comprehensive DICOM to NIfTI etc support
>> * Labelled axes for images, maybe via xarray
>> * Integrated API for surface formats [1]
>> * HDF5 serialization for many image formats
>> * Ability to read images directly from URLs, read / write images to /
>> from AWS, GCS, Azure data storage addresses [2]
>> * Optimized visualization for web and desktop
>>
>> Is there anything else you'd like to see?
>>
>> See you,
>>
>> Matthew
>>
>> [1] https://github.com/nipy/nibabel/issues/936
>> [2] c.f. https://pandas.pydata.org/pandas-docs/version/1.1.0/whatsnew/v1.1.0.html#fsspec-now-used-for-filesystem-handling
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>
>
>
> --
> Emanuele Olivetti, Ph.D.
> Senior Research Scientist at Bruno Kessler Foundation (FBK-ICT)
> NeuroInformatics Laboratory (NILab) http://nilab.fbk.eu
> Center for Mind and Brain Sciences (CIMeC), University of Trento
> Via delle Regole 101 - 38123 Mattarello (Trento), ITALY
> olivetti at fbk.eu - +39 0461314179
> emanuele.olivetti at unitn.it - +39 0461282760
>
>
>
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