xcp_d.utils.ingestion module

Functions to support ingestion of non-BIDS preprocessing derivatives.

xcp_d.utils.ingestion.collect_anatomical_files(anat_dir_orig, anat_dir_fmriprep, base_anatomical_ents)

Collect anatomical files from ABCD or HCP-YA derivatives.

xcp_d.utils.ingestion.collect_confounds(task_dir_orig, func_dir_fmriprep, base_task_ents, work_dir, bold_file, brainmask_file, csf_mask_file, wm_mask_file)

Create confound regressors.

xcp_d.utils.ingestion.collect_meshes(anat_dir_orig, anat_dir_fmriprep, sub_id, subses_ents)

Collect mesh files from ABCD or HCP-YA derivatives.

xcp_d.utils.ingestion.collect_morphs(anat_dir_orig, anat_dir_fmriprep, sub_id, subses_ents)

Collect and convert morphometry files to CIFTIs.

xcp_d.utils.ingestion.copy_file(src, dst)

Copy a file from source to dest.

source and dest must be file-like objects, i.e. any object with a read or write method, like for example StringIO.

xcp_d.utils.ingestion.copy_files_in_dict(copy_dictionary)

Copy files in dictionary.

xcp_d.utils.ingestion.extract_mean_signal(mask, nifti, work_dir)

Extract mean signal within mask from NIFTI.

xcp_d.utils.ingestion.plot_bbreg(fixed_image, moving_image, contour, out_file='report.svg')

Plot bbref_fig_fmriprep results.

xcp_d.utils.ingestion.write_json(data, outfile)

Write dictionary to JSON file.