Non topup

[akeshavan]

Don't merge yet! I just want you all to see what's in progress

[pep8speaks]

Hello @akeshavan! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file dmriprep/cli.py:

Line 76:17: E117 over-indented
Line 77:80: E501 line too long (84 > 79 characters)
Line 80:80: E501 line too long (84 > 79 characters)
Line 83:80: E501 line too long (101 > 79 characters)
Line 88:80: E501 line too long (106 > 79 characters)
Line 92:37: E128 continuation line under-indented for visual indent
Line 92:80: E501 line too long (84 > 79 characters)
Line 93:37: E128 continuation line under-indented for visual indent
Line 94:37: E128 continuation line under-indented for visual indent
Line 95:37: E128 continuation line under-indented for visual indent
Line 95:80: E501 line too long (84 > 79 characters)
Line 98:80: E501 line too long (81 > 79 characters)

• In the file dmriprep/io.py:

Line 29:80: E501 line too long (100 > 79 characters)
Line 36:80: E501 line too long (100 > 79 characters)
Line 63:80: E501 line too long (90 > 79 characters)
Line 64:80: E501 line too long (90 > 79 characters)

• In the file dmriprep/run.py:

Line 310:21: E128 continuation line under-indented for visual indent
Line 311:21: E128 continuation line under-indented for visual indent
Line 312:21: E128 continuation line under-indented for visual indent
Line 474:80: E501 line too long (86 > 79 characters)
Line 567:5: E303 too many blank lines (2)

Comment last updated at 2019-05-17 20:46:43 UTC

[akeshavan]

this is shady

[josephmje]

If the BIDSLayout object is passed, we can read the PhaseEncodingDirection and TotalReadoutTime with layout.get_metadata()

[akeshavan]

update on this! It failed at EddyQuad, which requires a param_file. Will look into this next week!

ValueError: EddyQuad requires a value for input 'param_file'. For a list of required inputs, see EddyQuad.help()