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

[Reid, Robert I. (Rob)]

Hi,

I third the tractogram request, at the risk of taking the thread off topic. Would it be in nibabel’s remit to add a function to view a tractogram as a 3D array of streamline counts per voxel? That way NIFTI viewers such as FSLeyes that are not (last I checked) set up as tractogram viewers a la trackvis, but are python powered, could load and display tractograms in a limited way on the fly. I sometimes find it handy to overlay tractogram with other images using a viewer that caters more to the traditional “2D” display mode with lots of overlay options than one that focuses on 3D renders.

I got a 404 error for Emanuele’s load_trk.py URL. Maybe things were rearranged?

Could near numpy performance without resampling be achieved by storing the tractogram as a dict of numpy arrays keyed by the number of points in their streamlines?
e.g. {20: <numpy array of all the streamlines with 20 points>, 21: <numpy array of all the streamlines with 21 points>, …}

Thanks,

Rob


From: Neuroimaging [mailto:neuroimaging-bounces+reid.robert=mayo.edu at python.org] On Behalf Of Emanuele Olivetti
Sent: Thursday, July 30, 2020 11:00 AM
To: Neuroimaging analysis in Python
Subject: [EXTERNAL] Re: [Neuroimaging] CZI grant - what would you like to see in Nibabel?

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<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

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<mailto: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<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>.

--
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/ed03486e/attachment-0001.html>