xcp_d.utils.utils module

Miscellaneous utility functions for xcp_d.

xcp_d.utils.utils.check_deps(workflow)[source]

Make sure dependencies are present in this system.

xcp_d.utils.utils.denoise_with_nilearn(preprocessed_bold, confounds, voxelwise_confounds, sample_mask, low_pass, high_pass, filter_order, TR, num_threads)[source]

A wrapper to call _denoise_with_nilearn using multiprocessing

xcp_d.utils.utils.estimate_brain_radius(mask_file, head_radius='auto')[source]

Estimate brain radius from binary brain mask file.

Parameters:

  • mask_file (str) – Binary brain mask file, in nifti format.

  • head_radius (float or “auto”) – Radius of the head, in millimeters, for framewise displacement calculation.

    xcp_d’s default head radius is 50. The recommended value for infants is 35. A value of ‘auto’ is also supported, in which case the brain radius is estimated from the preprocessed brain mask.

Returns:

brain_radius – Estimated brain radius, in millimeters.

Return type:

float

Notes

This function estimates the brain radius based on the brain volume, assuming that the brain is a sphere. This was Paul Taylor’s idea, shared in this NeuroStars post: https://neurostars.org/t/estimating-head-brain-radius-automatically/24290/2.

xcp_d.utils.utils.fwhm2sigma(fwhm)[source]

Convert full width at half maximum to sigma.

Parameters:

fwhm (float) – Full width at half maximum.

Returns:

Sigma.

Return type:

float

xcp_d.utils.utils.get_bold2std_and_t1w_xfms(bold_file, template_to_anat_xfm)[source]

Find transform files in reverse order to transform BOLD to MNI152NLin2009cAsym/T1w space.

Since ANTSApplyTransforms takes in the transform files as a stack, these are applied in the reverse order of which they are specified.

NOTE: This is a Node function.

Parameters:

  • bold_file (str) – The preprocessed BOLD file.

  • template_to_anat_xfm – The from field is assumed to be the same space as the BOLD file is in. The MNI space could be MNI152NLin2009cAsym, MNI152NLin6Asym, or MNIInfant.

Returns:

  • xforms_to_MNI (list of str) – A list of paths to transform files for warping to MNI152NLin2009cAsym space.

  • xforms_to_MNI_invert (list of bool) – A list of booleans indicating whether each transform in xforms_to_MNI indicating if each should be inverted (True) or not (False).

  • xforms_to_T1w (list of str) – A list of paths to transform files for warping to T1w space.

  • xforms_to_T1w_invert (list of bool) – A list of booleans indicating whether each transform in xforms_to_T1w indicating if each should be inverted (True) or not (False).

Notes

Only used for QCReport in init_postprocess_nifti_wf. QCReport wants MNI-space data in MNI152NLin2009cAsym.

xcp_d.utils.utils.get_std2bold_xfms(bold_file, source_file, source_space=None)[source]

Obtain transforms to warp atlases from a source space to the same template as the BOLD.

Since ANTSApplyTransforms takes in the transform files as a stack, these are applied in the reverse order of which they are specified.

NOTE: This is a Node function.

Parameters:

  • bold_file (str) – The preprocessed BOLD file.

  • source_file (str) – The source file to warp to the BOLD space.

  • source_space (str, optional) – The space of the source file. If None, the space of the source file is inferred and used.

Returns:

transforms – A list of paths to transform files.

Return type:

list of str

Notes

Used by:

  • to resample dseg in init_postprocess_nifti_wf for QCReport

  • to warp atlases to the same space as the BOLD data in init_functional_connectivity_nifti_wf

  • to resample dseg to BOLD space for the executive summary plots

Does not include inversion flag output because there is no need (yet). Can easily be added in the future.

xcp_d.utils.utils.is_number(s)[source]

Check if a string is a number.

xcp_d.utils.utils.list_to_str(lst)[source]

Convert a list to a pretty string.