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HCP pipelines improvements and diffusion #24

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HCP pipelines improvements and diffusion #24

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jokedurnez
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@jokedurnez jokedurnez commented Mar 12, 2018 •
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CHANGES:

  • updated bids-validator and pybids to latest versions
  • added support for Diffusion
  • added support for multiple fmaps
  • added new test data that follows bids structure (as imposed in latest bids validator)
  • pulls my version of the pipelines, for two reasons:
    • pipelines require gpu for diffusion (I switched that off)
    • several bugs because of inconsistensies between versions of connectome-workbench (published vs dev), freesurfer (5.3 vs 6),...

@jokedurnez
update bids validator
5057408
@jokedurnez
update bids validator
4670419
@jokedurnez
implement diffusion preprocessing
43f1541
@jokedurnez
debug outdir
c1da28f
@jokedurnez
merge
5ba0564 
Merge branch 'master' of https://github.com/jokedurnez/HCPPipelines
@jokedurnez
echo spacing units
fe69ca5
@jokedurnez
add data_is_shelled for dwi
41bd5f5
@jokedurnez
units of echo spacing
cc0eabc
@jokedurnez
update pybids
e205d7d
@jokedurnez
add eddy
278ecfb
@jokedurnez
return list of fieldmaps, debug echospacing
4e596fb
@jokedurnez
use jokes pipelines to check
1d87f1d
@jokedurnez
adapt to pybids 0.4.2 + add checks for consistency
3a30eaa
@jokedurnez
debug when fieldmaps are magnitude (hcp test)
49d523d
@jokedurnez
debug fieldmap with magnitude
25af78f
@jokedurnez
debug consistency check
1af0123
@jokedurnez
restore validator
e3c0294
@jokedurnez
update bids validator
a316145
@jokedurnez
update fsl to 5.0.10 to get surface processing working
2497e15
@jokedurnez
set MSMbindir, aka the ony reason why I'm doing these changes
105f768
@jokedurnez
missing FSLDIR
16832a8
@jokedurnez
connectome workbench link + typo
ac60bf6
@jokedurnez
update circleCI with new data
ef96dd7
@jokedurnez
update version number for tests
0cf56eb
@jokedurnez
change provider img
bd328c9
@jokedurnez
actually not using lifespan
19ab83c
@jokedurnez
trigger circle
2062945
@jokedurnez
add MSMCONFIGDIR
023e003
@jokedurnez
increase timeout for docker build after upgrading fsl
b08a02c
@jokedurnez
get right files on OSF
f809f93
@jokedurnez
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Sorry, the history is super messy.

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@jokedurnez