Hi @rsmith and others!
I’ve been using MRtrix3 outside of BIDSApps, but would like to try it out to save myself some scripting…
We have a lot of complicated diffusion WIPs and c2ps that don’t always convert nicely to BIDS (extra series all over the place), so I was wondering if you had an example of the minimum BIDS inputs I would need to get going with the MRtrix3 connectome BIDSApp? Is there perhaps an example dataset?
Thanks for all your help, and for the tools!
Welcome Thom!
That’s a difficult one, which really extends beyond MRtrix3_connectome to BIDS Apps in general. Firstly, depending on exactly what sequences you’re using, it’s possible that the type of data that you’re acquiring aren’t even yet within the BIDS specification, depending on their degree of exoticism. Secondly, there’s a deceptively large gap between having a data storage specification that is compatible with some form of data, and having an automated processing pipeline that can deal with absolutely anything thrown at it; so again, depending on how unusual your data are, there’s no guarantee that any specific tool will actually know what to do with it. I’m currently thinking in particular of arbitrary b-tensor encoding, which is currently supported neither by BIDS nor MRtrix3, let alone MRtrix3_connectome.
While there’s an example dataset that’s downloaded by that BIDS App for the sake of Continuous Integration testing, those data are intended to be used in a manner that skips pre-processing, so might not actually give you key pieces of information for preparing your own raw data.
What I would suggest instead, since it’s not something to be addressed within MRtrix3 itself, is to post an Issue over at the corresponding repository requesting me to upload some sample BIDS data (assuming nobody else here has such at hand?). If you think that there are confounds regarding your specific data that may make MRtrix3-based processing impossible over and above just doing a BIDS conversion, that would be appropriate to discuss on this forum, as in general I’ve tried to keep their scopes of compatibility consistent (though the BIDS App now needs an update to match 3.0.0); but it would depend on the particulars.
Cheers
Rob
Hi Rob,
Thanks for the detailed answer - I really appreciate it 
Yes, absolutely - our data is rarely BIDS spec compliant and we have to wrestle it into a BIDS-like format in order for anything to work with BIDSApps generally.
We do have some nice ‘easy’ 3T data that I think conforms to BIDS standard though, so I may try that first before going down the rabbit hole of our exotic 7T data.
My goal is for things to be easier while processing multiple datasets with different acquisition parameters from different scanners etc., so if the BIDSApp is maybe not the way to go I’m more than happy to use the tools here.
I’ll raise an issue though as it would be great to get an idea of what I need to get it running.
Cheers,
Tom