nipype.interfaces.fsl.aroma module

This commandline module provides classes for interfacing with the ICA-AROMA.py command line tool.

ICA_AROMA

Link to code

Bases: CommandLine

Wrapped executable: ICA_AROMA.py.

Interface for the ICA_AROMA.py script.

ICA-AROMA (i.e. ‘ICA-based Automatic Removal Of Motion Artifacts’) concerns a data-driven method to identify and remove motion-related independent components from fMRI data. To that end it exploits a small, but robust set of theoretically motivated features, preventing the need for classifier re-training and therefore providing direct and easy applicability.

See link for further documentation: https://github.com/rhr-pruim/ICA-AROMA

Example

>>> from nipype.interfaces.fsl import ICA_AROMA
>>> from nipype.testing import example_data
>>> AROMA_obj = ICA_AROMA()
>>> AROMA_obj.inputs.in_file = 'functional.nii'
>>> AROMA_obj.inputs.mat_file = 'func_to_struct.mat'
>>> AROMA_obj.inputs.fnirt_warp_file = 'warpfield.nii'
>>> AROMA_obj.inputs.motion_parameters = 'fsl_mcflirt_movpar.txt'
>>> AROMA_obj.inputs.mask = 'mask.nii.gz'
>>> AROMA_obj.inputs.denoise_type = 'both'
>>> AROMA_obj.inputs.out_dir = 'ICA_testout'
>>> AROMA_obj.cmdline  
'ICA_AROMA.py -den both -warp warpfield.nii -i functional.nii -m mask.nii.gz -affmat func_to_struct.mat -mc fsl_mcflirt_movpar.txt -o .../ICA_testout'
Mandatory Inputs:

  • denoise_type (‘nonaggr’ or ‘aggr’ or ‘both’ or ‘no’) – Type of denoising strategy: -no: only classification, no denoising -nonaggr (default): non-aggresssive denoising, i.e. partial component regression -aggr: aggressive denoising, i.e. full component regression -both: both aggressive and non-aggressive denoising (two outputs). Maps to a command-line argument: -den %s. (Nipype default value: nonaggr)

  • feat_dir (a pathlike object or string representing an existing directory) – If a feat directory exists and temporal filtering has not been run yet, ICA_AROMA can use the files in this directory. Maps to a command-line argument: -feat %s. Mutually exclusive with inputs: in_file, mat_file, fnirt_warp_file, motion_parameters.

  • in_file (a pathlike object or string representing an existing file) – Volume to be denoised. Maps to a command-line argument: -i %s. Mutually exclusive with inputs: feat_dir.

  • motion_parameters (a pathlike object or string representing an existing file) – Motion parameters file. Maps to a command-line argument: -mc %s. Mutually exclusive with inputs: feat_dir.

  • out_dir (a pathlike object or string representing a directory) – Output directory. Maps to a command-line argument: -o %s. (Nipype default value: out)

Optional Inputs:

  • TR (a float) – TR in seconds. If this is not specified the TR will be extracted from the header of the fMRI nifti file. Maps to a command-line argument: -tr %.3f.

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • dim (an integer) – Dimensionality reduction when running MELODIC (default is automatic estimation). Maps to a command-line argument: -dim %d.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • fnirt_warp_file (a pathlike object or string representing an existing file) – File name of the warp-file describing the non-linear registration (e.g. FSL FNIRT) of the structural data to MNI152 space (.nii.gz). Maps to a command-line argument: -warp %s. Mutually exclusive with inputs: feat_dir.

  • mask (a pathlike object or string representing an existing file) – Path/name volume mask. Maps to a command-line argument: -m %s. Mutually exclusive with inputs: feat_dir.

  • mat_file (a pathlike object or string representing an existing file) – Path/name of the mat-file describing the affine registration (e.g. FSL FLIRT) of the functional data to structural space (.mat file). Maps to a command-line argument: -affmat %s. Mutually exclusive with inputs: feat_dir.

  • melodic_dir (a pathlike object or string representing an existing directory) – Path to MELODIC directory if MELODIC has already been run. Maps to a command-line argument: -meldir %s.

Outputs:

  • aggr_denoised_file (a pathlike object or string representing an existing file) – If generated: aggressively denoised volume.

  • nonaggr_denoised_file (a pathlike object or string representing an existing file) – If generated: non aggressively denoised volume.

  • out_dir (a pathlike object or string representing an existing directory) – Directory contains (in addition to the denoised files): melodic.ica + classified_motion_components + classification_overview + feature_scores + melodic_ic_mni).