qsirecon.interfaces.gradients module

Handle merging and spliting of DSI files.

class qsirecon.interfaces.gradients.ExtractB0s(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Extract a b0 series and a mean b0 from a dwi series.

Mandatory Inputs:

dwi_series (a pathlike object or string representing an existing file)

Optional Inputs:

  • b0_indices (a list of items which are any value)

  • b0_threshold (an integer) – (Nipype default value: 50)

  • bval_file (a pathlike object or string representing an existing file)

Outputs:

  • b0_average (a pathlike object or string representing an existing file)

  • b0_series (a pathlike object or string representing an existing file)

class qsirecon.interfaces.gradients.GradientSelect(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

  • bval_file (a pathlike object or string representing an existing file)

  • bvec_file (a pathlike object or string representing an existing file)

  • dwi_file (a pathlike object or string representing an existing file)

  • requested_shells (a list of items which are an integer or ‘highest’ or ‘lowest’)

Optional Inputs:

  • b_file (a pathlike object or string representing an existing file)

  • btable_file (a pathlike object or string representing an existing file)

  • bval_distance_cutoff (a float) – (Nipype default value: 5.0)

  • expected_n_input_shells (an integer)

Outputs:

  • b_file (a pathlike object or string representing an existing file)

  • btable_file (a pathlike object or string representing an existing file)

  • bval_file (a pathlike object or string representing an existing file)

  • bvec_file (a pathlike object or string representing an existing file)

  • dwi_file (a pathlike object or string representing an existing file)

  • local_bvec_file (a pathlike object or string representing an existing file)

class qsirecon.interfaces.gradients.RemoveDuplicates(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

  • bval_file (a pathlike object or string representing an existing file)

  • bvec_file (a pathlike object or string representing an existing file)

  • dwi_file (a pathlike object or string representing an existing file)

Optional Inputs:

  • b_file (a pathlike object or string representing an existing file)

  • btable_file (a pathlike object or string representing an existing file)

  • distance_cutoff (a float) – (Nipype default value: 5.0)

  • expected_directions (an integer)

  • local_bvec_file (a pathlike object or string representing an existing file)

Outputs:

  • b_file (a pathlike object or string representing an existing file)

  • btable_file (a pathlike object or string representing an existing file)

  • bval_file (a pathlike object or string representing an existing file)

  • bvec_file (a pathlike object or string representing an existing file)

  • dwi_file (a pathlike object or string representing an existing file)

  • local_bvec_file (a pathlike object or string representing an existing file)

qsirecon.interfaces.gradients.concatenate_bvals(bval_list, out_file)[source]

Create an FSL-style bvals file from split bval files.

qsirecon.interfaces.gradients.concatenate_bvecs(input_files)[source]

Create Dipy-style gradient array (3-columns) from bvec files.

qsirecon.interfaces.gradients.subset_dwi(original_bval, original_bvec, original_b, original_btable, original_nifti, indices, newdir, suffix='_bsel')[source]

Create a subset of a dwi based on a set of indices.