xcp_d.interfaces.plotting.QCPlots

class xcp_d.interfaces.plotting.QCPlots(from_file=None, resource_monitor=None, **inputs)[source]

Generate pre- and post-processing quality control (QC) figures.

Examples

>>> from tempfile import TemporaryDirectory
>>> tmpdir = TemporaryDirectory()
>>> os.chdir(tmpdir.name)
.. doctest::
qcplots = QCPlots()
qcplots.inputs.cleaned_file = datafile
qcplots.inputs.name_source = rawbold
qcplots.inputs.bold_file = rawbold
qcplots.inputs.TR = TR
qcplots.inputs.temporal_mask = temporalmask
qcplots.inputs.mask_file = mask
qcplots.inputs.dummy_scans = dummy_scans
qcplots.run()
.. testcleanup::
>>> tmpdir.cleanup()
Mandatory Inputs:

  • TR (a float) – Repetition Time.

  • bold_file (a pathlike object or string representing an existing file) – Preprocessed BOLD file, after dummy scan removal. Used in carpet plot.

  • cleaned_file (a pathlike object or string representing an existing file) – Processed file, after denoising and censoring.

  • dummy_scans (an integer) – Dummy time to drop.

  • fmriprep_confounds_file (a pathlike object or string representing an existing file) – FMRIPrep confounds file, after dummy scans removal.

  • head_radius (a float) – Head radius for FD calculation.

  • mask_file (a pathlike object or string representing an existing file or None) – Mask file from nifti. May be None, for CIFTI processing.

  • name_source (a pathlike object or string representing a file) – Preprocessed BOLD file. Used to find files. In the case of the concatenation workflow, this may be a nonexistent file (i.e., the preprocessed BOLD file, with the run entity removed).

  • temporal_mask (a pathlike object or string representing an existing file) – Temporal mask.

Optional Inputs:

  • anat_brainmask (a pathlike object or string representing an existing file) – Mask in T1W.

  • bold2T1w_mask (a pathlike object or string representing an existing file) – Bold mask in MNI.

  • bold2temp_mask (a pathlike object or string representing an existing file) – Bold mask in T1W.

  • seg_file (a pathlike object or string representing an existing file) – Seg file for nifti.

  • template_mask (a pathlike object or string representing an existing file) – Template mask.

Outputs:

  • clean_qcplot (a pathlike object or string representing an existing file) – Qc plot after regression.

  • qc_file (a pathlike object or string representing an existing file) – Qc file in tsv.

  • raw_qcplot (a pathlike object or string representing an existing file) – Qc plot before regression.

__init__(from_file=None, resource_monitor=None, **inputs)[source]

Subclasses must implement __init__

Methods

__init__([from_file, resource_monitor])

Subclasses must implement __init__

aggregate_outputs([runtime, needed_outputs])

Collate expected outputs and apply output traits validation.

help([returnhelp])

Prints class help

load_inputs_from_json(json_file[, overwrite])

A convenient way to load pre-set inputs from a JSON file.

run([cwd, ignore_exception])

Execute this interface.

save_inputs_to_json(json_file)

A convenient way to save current inputs to a JSON file.

Attributes

always_run

Should the interface be always run even if the inputs were not changed? Only applies to interfaces being run within a workflow context.

can_resume

Defines if the interface can reuse partial results after interruption.

resource_monitor

version

interfaces should implement a version property