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

Christopher Markiewicz markiewicz at stanford.edu
Mon Aug 3 12:52:29 EDT 2020

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 Nibabel?


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

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


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