BIDS import/export, bet_premask bug fix, new modules - #115

Could you, please, make sure that the function header in aamod_meanstructural.m (line 1) is consitent with the function name?

Done.

I have tested the relevant functions (reading and writing BIDS), and they are working as usual. Though, I have not tested the new features and modules. I suggest to come up with relevant examples. However, if you are confident enough, I am happy to merge the PR.

Small glitch: I believe there's a typo in the report generation in the firstlevel_model modules -- the jpegs that get created during analysis are named diagnostics_... (note the "s") and the report generation looks for files named diagnostic_... The (current) single-file version of aamod_firstlevel_model.m has the same glitch.

There's also currently quite a number of firstlevel module variants in the distribution. As a new user, I found this rather confusing. Might we want to think about organizing these (or culling ones that are more "experimental") in the spirit of trying to make aa more user friendly?

Ok, I had no idea reports work in that way. I ran a grep diagnostics_ aa_modules/*.m and changed accordingly. Better now?

Re models, I think fMRI necessarily involves a huge number of custom first level models. That's where almost all the theoretically interesting stuff happens (the second level model is usually just RFX on the summary stats). The alternative is to try to cover all the unusual model cases in one monolithic aamod_firstlevel_model, but I think that's actually more confusing. For one thing you would need to look at the module settings to know what kind of model was run, whereas with custom modules you can see immediately from the task list what was done.

So I think we should have many first level models, but perhaps we need to add more documentation to clarify exactly what each variant is doing. For instance, the models I added now have lots of comments discussing what they are for, and pointing out that you may prefer aamod_firstlevel_model for standard use cases.

Ok, I had no idea reports work in that way. I ran a grep diagnostics_ aa_modules/*.m and changed accordingly. Better now?

I checked the new diffs and they look good to me. Thanks.

Also, I see your point about providing useful custom modules (for first level analysis and in general).

So we are all good to merge then @tiborauer?