Adds utilities for preparing the data for eddy and analysis

designer.preprocessing.preparation.fix_bval(bvalfile)

Converts all whitespace into newlines in the file

Parameters

bvalfile (str) – The .bval to ensure is the correct format for mrtrix

Returns

Return type

None, overwrites bval

designer.preprocessing.preparation.make_se_epi(filetable)

Makes a single spin-echo epi from the topup and the dwi

Parameters

filetable (dict of str) – The filetable that pydesigner.py uses to track files

Returns

Return type

None, writes file

designer.preprocessing.preparation.make_simple_mif(filetable)

Makes a single .mif from the HEAD dwi file

Parameters

filetable (dict of str) – The filetable that pydesigner.py uses to track files

Returns

Return type

None, writes file