[WIP, FIX] remove bold_mask generation from t2s

[emdupre]

Changes proposed in this pull request

Addresses #1786

Removes bold_mask generation from bold_t2s_wf in the case of multi-echo data.

Documentation that should be reviewed

N/A.

[emdupre]

This code is passing locally, and it seems like the errors here are in the cache:

FileNotFoundError: [Errno 2] No such file or directory: 'result_csf_msk.pklz'

or due to build time-out:

Too long with no output (exceeded 2h0m0s)

I'll try to clear the cache and re-run.

[effigies]

@emdupre I'm not sure this is a cache issue. Can you try updating the nipype requirement in setup.cfg to:

nipype @ git+https://github.com/effigies/nipype.git@e206f3d53198c683e959fe1e73426ce5cf362b93

[emdupre]

Thanks for the pin, @effigies ! That worked perfectly 👍

The brain masks here for ds210 don't look great, but they do locally for some data @Shotgunosine shared. Should I run (a non-downsampled) ds210 locally as well to confirm ?

[effigies]

@emdupre Yeah, I would go ahead and check on full-resolution (though you might want to truncate to ~40 TRs to save time).

[Shotgunosine]

Yeah, those maps do look problematic, hopefully they'll look better on full resolution. It looks like it's mostly including skull as opposed to excluding brain, which is a less drastic error I think.

[effigies]

@emdupre I merged master, so you'll want to pull before doing anything else. Feel free to rebase, if you'd rather not have the pin and merge in the history,

[emdupre]

Superceded by #2109