qsiprep.workflows.dwi.util module

Utility workflows

qsiprep.workflows.dwi.util.init_dwi_reference_wf(dwi_file=None, name='dwi_reference_wf', gen_report=False, source_file=None, desc='initial')

Create dwiref reference image.

If register_t2, a skull-stripped T1w image is downsampled to the resolution of the b=0 input image and registered to it.

(Source code)

Parameters:

• dwi_file (str, optional) – A b=0 image Default is None.

• name (str) – Name of workflow (default: dwi_reference_wf)

• gen_report (bool, optional) – Whether a mask report node should be appended in the end. Default is False.

• source_file (str, optional) – Source file for the mask report. Default is None.

• desc (str, optional) – Description of the dwi reference image. Default is initial.

Inputs:

• b0_template – the b0 template used as the motion correction reference

• t1_brain – skull-stripped T1w image from the same subject

• t1_mask – mask image for t1_brain

• wm_seg – white matter segmentation from the T1w image

Outputs:

• raw_ref_image – Reference image to which dwi series is motion corrected

• ref_image – Contrast-enhanced reference image

• ref_image_brain – Skull-stripped reference image

• dwi_mask – Skull-stripping (rough) mask of reference image

• validation_report – HTML reportlet indicating whether dwi_file had a valid affine

See also

• init_enhance_and_skullstrip_wf()

qsiprep.workflows.dwi.util.get_source_file(dwi_files, output_prefix=None, suffix='')

The reportlets need a source file. This file might not exist in the input data.

qsiprep.workflows.dwi.util.init_dwi_reference_wf(dwi_file=None, name='dwi_reference_wf', gen_report=False, source_file=None, desc='initial')

Create dwiref reference image.

If register_t2, a skull-stripped T1w image is downsampled to the resolution of the b=0 input image and registered to it.

(Source code)

Parameters:

• dwi_file (str, optional) – A b=0 image Default is None.

• name (str) – Name of workflow (default: dwi_reference_wf)

• gen_report (bool, optional) – Whether a mask report node should be appended in the end. Default is False.

• source_file (str, optional) – Source file for the mask report. Default is None.

• desc (str, optional) – Description of the dwi reference image. Default is initial.

Inputs:

• b0_template – the b0 template used as the motion correction reference

• t1_brain – skull-stripped T1w image from the same subject

• t1_mask – mask image for t1_brain

• wm_seg – white matter segmentation from the T1w image

Outputs:

• raw_ref_image – Reference image to which dwi series is motion corrected

• ref_image – Contrast-enhanced reference image

• ref_image_brain – Skull-stripped reference image

• dwi_mask – Skull-stripping (rough) mask of reference image

• validation_report – HTML reportlet indicating whether dwi_file had a valid affine

See also

• init_enhance_and_skullstrip_wf()