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

[Christopher Markiewicz]

Thanks, Gael! This is very helpful.
________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Gael Varoquaux <gael.varoquaux at normalesup.org>
Sent: Monday, August 3, 2020 5:58 PM
To: Neuroimaging analysis in Python <neuroimaging at python.org>
Subject: Re: [Neuroimaging] Neuroimaging package stats (was RE: CZI grant - what would you like to see in Nibabel?)

Python usage figures updated for this year:
https://twitter.com/GaelVaroquaux/status/1263413593615273986
(same methodology as the paper).

G

On Mon, Aug 03, 2020 at 11:45:43PM +0200, Gael Varoquaux wrote:
> Hi Chris,

> With regards to situating the usage on the Python stack in neuroimaging,
> you may be interested in the evaluation that I did for our Annual Reviews
> paper on Neuroimaging software tools, fig 2 in:
> https://www.annualreviews.org/doi/full/10.1146/annurev-biodatasci-072018-021237

> The methodology involved manually recording the number of answers with a
> year limitation to a well specified query on Google scholar.

> HTH,

> G

> On Mon, Aug 03, 2020 at 04:52:29PM +0000, Christopher Markiewicz 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.

> > Best,
> > Chris

> > ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
> > 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 Nibabel?

> > Hi,

> > On Sat, Aug 1, 2020 at 1:27 PM Samuel St-Jean <stjeansam at gmail.com> wrote:

> > > 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
> > know.

> > > 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
> > this?

> > We can then link to relevant stuff like the JSON header NEP, and
> > Brendon's stuff about dcmstack, possible xarray integration.

> > Cheers,

> > Matthew
> > _______________________________________________
> > 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
--
    Gael Varoquaux
    Research Director, INRIA              Visiting professor, McGill
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux
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