[Neuroimaging] Neuroimaging package stats (was RE: CZI grant - what would you like to see in Nibabel?)

Yaroslav Halchenko yoh at onerussian.com
Mon Aug 3 21:58:39 EDT 2020

Fwiw, since not really a comparison asked for. According to https://libraries.io/pypi/nibabel/sourcerank rank is 20! Psychopy (supported by czi) is 9. Pip 23.
Nibabel is THE core package for neuroimaging in Python, like numpy for numeric computation in general (rank 29). Python adoption in neuroimaging grows, and with that the use of nibabel since there simply no alternative.

On August 3, 2020 12:52:29 PM EDT, Christopher Markiewicz <markiewicz at stanford.edu> wrote:
>Hi all,
>Following up on the CZI discussion, for the grant we need to situate
>NiBabel in the neuroimaging world. I suspect some Nipy projects might
>have recently compiled some kind of usage metrics of their packages and
>the non-Nipy packages (SPM, FSL, AFNI, FreeSurfer, ANTs, ITK-SNAP?)
>that we're "competing" with.
>If anybody has this kind of data, or knows off-hand where to find it, I
>would appreciate any help you can give.
>From: Neuroimaging
><neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of
>Matthew Brett <matthew.brett at gmail.com>
>Sent: Saturday, August 1, 2020 8:32 AM
>To: Neuroimaging analysis in Python <neuroimaging at python.org>
>Subject: Re: [Neuroimaging] CZI grant - what would you like to see in
>On Sat, Aug 1, 2020 at 1:27 PM Samuel St-Jean <stjeansam at gmail.com>
>> Even before talking multimodality, it would be useful to have
>something multi MRI weighting. As of now you have the bval/bvec for
>diffusion you need to carry around, if you are a bit fancy you have the
>gradient timings an other things, and if you use non spin-echo stuff
>you also need to carry around another layer of information. Other stuff
>like fmri seems to also carry around relevant info, and you can add to
>the game relaxometry experiments (I'd guess inversion time, flip angle
>and other things for T1 mapping for example), and if you play with more
>advanced diffusion sequences you have new data structures you need to
>> That's a lot of side files that can go around beyond your everyday
>nifti. And pretty much every tool uses his own internal format to keep
>track of all that because of this (on top of my mind there is .mif for
>mrtrix, exploredti stash everything in a matlab file after conversion,
>there is also an .xps format also for advanced diffusion with is using
>matlab, probably others).  I personally started stashing everything in
>a json file for convenience, but having a flexible, throw everything in
>it file would definitely be useful, and could potentially be used by
>other software, making mixing tools far easier if everything was read
>from a central file, just as now it is easy to go around with a nifti,
>bval and bvec files.
>> So I'd vote for something similar, say based on json because it is
>somewhat readable and standard, which would record relevant
>experimental info (similar to what dcm2niix does I'd guess, but with
>only the necessary info). It would also make it easy to add new stuff
>in it over time. I have a rough and barebone xps to json converter I
>made somewhere if it can serve and an example of what I mean.
>Thanks for this.   Would you mind opening an issue on the lines of
>"Attach metadata to images, and record on disk" with text a bit like
>We can then link to relevant stuff like the JSON header NEP, and
>Brendon's stuff about dcmstack, possible xarray integration.
>Neuroimaging mailing list
>Neuroimaging at python.org

Yaroslav O. Halchenko (mobile version)
Center for Open Neuroscience   http://centerforopenneuroscience.org
Dartmouth College, NH, USA
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