import os
from pkg_resources import resource_filename as pkgrf
from xcp_d.utils.bids import collect_data from xcp_d.workflow.bold import init_boldpostprocess_wf
fmri_dir = pkgrf('xcp_d', 'data/fmriprep') layout, subj_data = collect_data( bids_dir=fmri_dir, input_type="fmriprep", participant_label='colornest001', task='rest', bids_validate=False, )
- bold_file = pkgrf(
'xcp_d', 'data/fmriprep/sub-colornest001/ses-1/func/sub-colornest001_ses-1_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz',
) custom_confounds_folder = pkgrf('xcp_d', 'data/fmriprep/sub-colornest001/ses-1/func/')
tseg = pkgrf('xcp_d', 'data/fmriprep/sub-colornest001/ses-1/anat/sub-colornest001_ses-1_rec-refaced_desc-preproc_T1w.nii.gz') t1w = pkgrf('xcp_d', 'data/fmriprep/sub-colornest001/ses-1/anat/sub-colornest001_ses-1_rec-refaced_dseg.nii.gz')
- wf = init_boldpostprocess_wf(
bold_file=bold_file, bandpass_filter=True, upper_bpf=0.08, lower_bpf=0.01, bpf_order=2, motion_filter_order=4, motion_filter_type=None, band_stop_min=0., band_stop_max=0., smoothing=6, head_radius=50., params='27P', custom_confounds_folder=custom_confounds_folder, omp_nthreads=1, dummy_scans=0, output_dir='output_dir', fd_thresh=0.2, n_runs=1, layout=layout, input_type, despike=False, dummytime=0, dcan_qc=False, name='bold_postprocess_wf',
) wf.inputs.inputnode.t1w = t1w wf.inputs.inputnode.t1seg = tseg