import os
from pkg_resources import resource_filename as pkgrf
from xcp_d.utils.bids import collect_data, extract_t1w_seg, select_registrationfile 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, participant_label='sub-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 = pkgrf( 'xcp_d', 'data/fmriprep/sub-colornest001/ses-1/func/sub-colornest001_ses-1_task-rest_run-1_desc-confounds_timeseries.tsv', )
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=str(bold_file), bandpass_filter=True, upper_bpf=0.08, lower_bpf=0.01, bpf_order=2, motion_filter_order=4, motion_filter_type='notch', band_stop_min=0., band_stop_max=0., smoothing=6, head_radius=50., params='27P', custom_confounds=custom_confounds, omp_nthreads=1, dummytime=0, output_dir='output_dir', fd_thresh=0.2, n_runs=1, layout=layout, despike=False, name='bold_postprocess_wf',
) wf.inputs.inputnode.t1w = t1w wf.inputs.inputnode.t1seg = tseg