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

[Emanuele Olivetti]

Will do. Most probably tomorrow.

Cheers,

Emanuele

On Thu, Jul 30, 2020 at 6:15 PM Matthew Brett <matthew.brett at gmail.com>
wrote:

> 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
> >> _______________________________________________
> >> Neuroimaging mailing list
> >> Neuroimaging at python.org
> >> https://mail.python.org/mailman/listinfo/neuroimaging
> >
> >
> >
> > --
> > 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
> >
> >
> >
> > FBK vi invita a leggere il suo Piano di rientro | FBK invites you to
> read its Premises Reopening Plan.
> >
> > --
> > Le informazioni contenute nella presente comunicazione sono di natura
> privata e come tali sono da considerarsi riservate ed indirizzate
> esclusivamente ai destinatari indicati e per le finalità strettamente
> legate al relativo contenuto. Se avete ricevuto questo messaggio per
> errore, vi preghiamo di eliminarlo e di inviare una comunicazione
> all’indirizzo e-mail del mittente.
> > --
> > The information transmitted is intended only for the person or entity to
> which it is addressed and may contain confidential and/or privileged
> material. If you received this in error, please contact the sender and
> delete the material.
> > _______________________________________________
> > 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
>

-- 
_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>._



--
Le informazioni contenute nella presente comunicazione sono di natura 
privata e come tali sono da considerarsi riservate ed indirizzate 
esclusivamente ai destinatari indicati e per le finalità strettamente 
legate al relativo contenuto. Se avete ricevuto questo messaggio per 
errore, vi preghiamo di eliminarlo e di inviare una comunicazione 
all’indirizzo e-mail del mittente.

--
The information transmitted is 
intended only for the person or entity to which it is addressed and may 
contain confidential and/or privileged material. If you received this in 
error, please contact the sender and delete the material.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/neuroimaging/attachments/20200730/ac144407/attachment.html>