Completed on 9 Oct 2017 by Krzysztof Jacek Gorgolewski .
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The paper entitled “AFQ-‐Browser: Supporting reproducible human neuroscience research through browser-‐based visualization tools” is a beautifully written description of a software tool that takes outputs a specific of a specific diffusion MRI analysis method (AFQ) and creates interactive visualizations that make data exploration easy. The tool implements some truly innovative ideas such as piggy backing on GitHub as a service for hosting data and visualizations and representation of data in a form that is appealing to data scientists with no prior MR experience. I hope that other tools will emulate those features. The manuscript also includes thoughtful discussion of exploratory vs hypothesis driven methods.
- The abstract gives the reader the wrong impression that the AFQ-Browser tool is more generic than it really is. It should be clarified that the tool only allows users to visualize and share outputs of AFQ analyses.
- When describing BrainBrowser and its involvement in MACACC dataset surely you meant “visualization” not “analysis”.
- It might be worth to introduce the publication feature earlier in the paper. I was quite confused when reading about reproducibility and data sharing without knowing that AFQ-Browser is not just a visualization tool.
- Please mention in the paper the license under which the tool is distributed and any pending or obtained patents that would limit its use or redistribution.
- If all AFQ users start uploading their results to GitHub using AFQ-Browser it might be hard to find or aggregate those results. It might be worth considering (and discussing) a centralized index (also hosted on GitHub) of all publicly available AFQ-Browser generated bundles. This index can be automatically updated during the “publish” procedure.
- GitHub is a great resource, but have few guarantees in terms of long term storage. A solution to this would be depositing the bundles into Zenodo which could be done directly from GitHub. Would be worth implementing and/or discussing this in the manuscript.
- It’s a technical detail, but it took me a little time to figure out why the tool requires user to spin up a local server (presumably to be able to access CSV and JSON files). Might be worth elaborating.
- Saving the visualization “view” (or “browser state”) seems cumbersome when done via a file. Could the view be encoded in the URL (via GET parameters)? Sharing of such views would be much easier and natural.
- Some example analyses include information about group membership or demographic information such as age. How is such information stored and conveyed to AFQ-Browser? Does it also come as output of AFQ?
- In the manuscript you mention that AFQ-Browser allows users to compare their results with normative distributions. Where are they coming from a central repository (please describe how it is populated) or do users need to provide such distributions themselves?
- It might be worth considering a crowdsourcing scheme such as the one employed in MRIQC Web API (https://mriqc.nimh.nih.gov/) to generate normative distributions of AFQ outputs.
- Is the way you store data in CSV files and their relation to the JSON files (beyond the “tidy” convention) described somewhere in detail? It would be useful for users.
- Please describe the software testing approach you employed in this project.