First working version of app

[Lestropie]

Adding some details so that @chrisfilo (and anybody else who stumbles across this) can see what is required to get a baseline version of the app running. List may be altered as I test & adjust minimal requirements.

• Finish MRtrix3 developments that will enable DWI pre-processing to be run without a priori knowledge of the phase-encoding design of either DWI or EPI SE field-mapping protocols, by reading this information from the image headers when available and passing this information to FSL's topup / eddy accordingly.
• Testing of both participant and group-level analyses (which will involve inter-subject connection density normalisation followed by calculation of the group average connectome).

[Lestropie]

Update: DWI pre-processing is working. Currently participant level analysis makes it to parcellation: CircleCI times out on recon-all after 2 hours, and FreeSurfer seems to be hanging indefinitely when run on my local container (need to dig deeper here). Have changed the CircleCI test to use the AAL parcellation. Initial 'version' of App (at least that is present when the BIDS Apps manuscript is submitted) will likely have the group level analysis disabled; but the bulk of the content in this analysis is yet unpublished anyways.

[chrisgorgo]

Good news! I would keep CircleCI minimalistic. For Freesurfer app I only
run autorecon1 - just to check if it will not break.

On Wed, Sep 21, 2016 at 8:16 PM, Robert Smith notifications@github.com
wrote:

Update: DWI pre-processing is working. Currently participant level
analysis makes it to parcellation: CircleCI times out on recon-all after
2 hours, and FreeSurfer seems to be hanging indefinitely when run on my
local container (need to dig deeper here). Have changed the CircleCI test
to use the AAL parcellation. Initial 'version' of App (at least that is
present when the BIDS Apps manuscript is submitted) will likely have the
group level analysis disabled; but the bulk of the content in this analysis
is yet unpublished anyways.

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[Lestropie]

@chrisfilo

The box is green. :-D

Group level testing is disabled because I'm still tinkering, but it's actually not too far away, and the app can very much be used without group-level analysis.

Rob