.. automodule:: xcp_d.workflow.bold
.. workflow::
:graph2use: orig
:simple_form: yes
import os
from pkg_resources import resource_filename as pkgrf
from xcp_d.utils import collect_data,select_registrationfile,extract_t1w_seg
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)
regfile = pkgrf('xcp_d','data/fmriprep/sub-colornest001/ses-1/anat/sub-colornest001_ses-1_rec-refaced_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5')
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')
from xcp_d.workflow.bold import init_boldpostprocess_wf
wf = init_boldpostprocess_wf(
bold_file = str(bold_file),
upper_bpf=0.08,
lower_bpf =0.01,
bpf_order=2,
motion_filter_order=4,
motion_filter_type='notch',
band_stop_min=0.1,
band_stop_max=0.2,
smoothing=5,
head_radius=50,
params='27P',
custom_confounds=custom_confounds,
omp_nthreads=1,
dummytime=0,
output_dir='output_dir',
fd_thresh=0.3,
num_bold=1,
layout=layout,
mni_to_t1w=regfile,
despike=None,
name='bold_postprocess_wf')
wf.inputs.inputnode.t1w = t1w
wf.inputs.inputnode.t1seg = tseg
.. automodule:: xcp_d.workflow.cifti