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

Franco Pestilli frakkopesto at gmail.com
Thu Jul 30 12:05:03 EDT 2020


- I second Emanuele’s suggestion.
- I would like to add and a community based proposal for a format for tractography it is becoming a necessity.

Best regards,
Franco

FRANCO PESTILLI, PhD | Associate Professor
Department of Psychology <https://liberalarts.utexas.edu/psychology/index.php> | College of Liberal Arts <https://liberalarts.utexas.edu/> | The University of Texas at Austin <https://www.utexas.edu/>
he/him | pestilli at utexas.edu <mailto:pestilli at utexas.edu> | web <https://liberalarts.utexas.edu/psychology/faculty/fp4834> | github <https://github.com/francopestilli> | brainlife.io  <https://brainlife.io/>

> On Jul 30, 2020, at 10:59 AM, 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 <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 <mailto: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 <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 <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 <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 <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 <mailto:olivetti at fbk.eu> - +39 0461314179
> emanuele.olivetti at unitn.it <mailto:emanuele.olivetti at unitn.it> - +39 0461282760
> 
> 
> 
> FBK vi invita a leggere il suo Piano di rientro <https://trasparenza.fbk.eu/COVID-19-comunicazioni-del-Datore-di-Lavoro-raccomandazioni-e-altro/Piano-di-rientro-FBK/Piano-di-rientro-FBK> | FBK invites you to read its Premises Reopening Plan <https://trasparenza.fbk.eu/COVID-19-comunicazioni-del-Datore-di-Lavoro-raccomandazioni-e-altro/Piano-di-rientro-FBK/English-version_FBK-Reopening-Plan>.
> 
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