aslprep.workflows.asl.confounds module

Workflows for calculating confounds for ASL data.

init_asl_confs_wf(mem_gb, name='asl_confs_wf')[source]

Build a workflow to generate and write out confounding signals.

This workflow calculates confounds for a asl series, and aggregates them into a TSV file, for use as nuisance regressors in a GLM. The following confounds are calculated, with column headings in parentheses:

  1. DVARS - original and standardized variants (dvars, std_dvars)

  2. Framewise displacement, based on head-motion parameters (framewise_displacement)

  3. Estimated head-motion parameters, in mm and rad (trans_x, trans_y, trans_z, rot_x, rot_y, rot_z)

Workflow Graph
../_images/aslprep-workflows-asl-confounds-1.png

(Source code, png, svg, pdf)

Parameters:

  • mem_gb (float) – Size of asl file in GB - please note that this size should be calculated after resamplings that may extend the FoV

  • metadata (dict) – BIDS metadata for asl file

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

Inputs:

  • asl – asl image, after the prescribed corrections (STC, HMC and SDC) when available.

  • asl_mask – asl series mask

  • movpar_file – SPM-formatted motion parameters file

  • rmsd_file – Framewise displacement as measured by fsl_motion_outliers.

  • skip_vols – number of non steady state volumes

  • t1w_mask – Mask of the skull-stripped template image

  • t1w_tpms – List of tissue probability maps in T1w space

  • t1_asl_xform – Affine matrix that maps the T1w space into alignment with the native asl space

Outputs:

  • confounds_file – TSV of all aggregated confounds

  • confounds_metadata – Confounds metadata dictionary.

init_carpetplot_wf(mem_gb, metadata, name='asl_carpet_wf')[source]

Build a workflow to generate carpet plots.

Resamples the MNI parcellation (ad-hoc parcellation derived from the Harvard-Oxford template and others).

Parameters:

  • mem_gb (float) – Size of ASL file in GB - please note that this size should be calculated after resamplings that may extend the FoV

  • metadata (dict) – BIDS metadata for ASL file

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

Inputs:

  • asl – asl image, after the prescribed corrections (STC, HMC and SDC) when available.

  • asl_mask – ASL series mask

  • confounds_file – TSV of all aggregated confounds

  • t1_asl_xform – Affine matrix that maps the T1w space into alignment with the native ASL space

  • std2anat_xfm – ANTs-compatible affine-and-warp transform file

Outputs:

out_carpetplot – Path of the generated SVG file