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danlurie/acompcor_lesionfix_workflow.py

Created August 23, 2021 02:35
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acompcor_lesionfix_workflow.py
import os
import sys
import nipype.interfaces.io as nio
import nipype.pipeline.engine as pe
from nipype import Node, Function
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from nipype.utils.filemanip import loadpkl
from niworkflows.interfaces.bids import BIDSDataGrabber
from niworkflows.utils.bids import collect_data
import pdb
def subtract_roi(in_mask, roi_file, out_dir):
import numpy as np
import nibabel as nb
import os
from nipype.utils.filemanip import fname_presuffix
msk = nb.load(in_mask)
mskdata = msk.get_data().astype(np.uint8)
roi = np.invert(nb.load(roi_file).get_data().astype(np.bool))
mskdata = mskdata * roi
msk.set_data_dtype(np.uint8)
out = os.path.join(out_dir, fname_presuffix(os.path.basename(in_mask), suffix='_roimsk'))
msk.__class__(mskdata, msk.affine, msk.header).to_filename(out)
return out
sub_id, deriv_dir = sys.argv[1:3]
fmriprep_ss_work_dir = os.path.join(deriv_dir, 'fmriprep/work/fmriprep_wf',
'single_subject_{0}_wf'.format(str(sub_id)))
# Create and configure a workflow
acompcor_lesionfix_wf = Workflow(name="acompcor_lesionfix_wf")
acompcor_lesionfix_wf.base_dir = os.path.join(deriv_dir,'acompcor_lesionfix/work')
# Load the bidssrc DataGrabber node from FMRIPREP
bidssrc_old = loadpkl(os.path.join(fmriprep_ss_work_dir,'bidssrc/_node.pklz'.format(sub_id)))
bidssrc_old_res = bidssrc_old.run()
# Loop through the functional scans found by bidssrc
for scan_path in bidssrc_old_res.outputs.bold:
scan_suffix = scan_path.split('_',1)[1].split('_bold')[0].replace('-', '_')
# Clone and reconfigure the bidssrc DataGrabber node from FMRIPREP
bidssrc_lf = bidssrc_old.clone(name="bidssrc_lf")
bidssrc_lf.base_dir = str(acompcor_lesionfix_wf.base_dir)
bidssrc_lf._output_dir = os.path.join(str(acompcor_lesionfix_wf.base_dir),
bidssrc_lf._output_dir.split('fmriprep_wf/',1)[1])
# Load, clone and reconfigure the acc_tfm node from FMRIPREP
acc_tfm_old = loadpkl(os.path.join(fmriprep_ss_work_dir,
'func_preproc_{0}_wf'.format(scan_suffix),'bold_confounds_wf/acc_tfm/_node.pklz'))
acc_tfm_lf = acc_tfm_old.clone(name='acc_tfm_lf')
acc_tfm_lf.base_dir = str(acompcor_lesionfix_wf.base_dir)
acc_tfm_lf._output_dir = os.path.join(str(acompcor_lesionfix_wf.base_dir),
acc_tfm_lf._output_dir.split('fmriprep_wf/',1)[1])
# Initialize and configure the subtract_roi node
subtract_roi_node = Node(Function(input_names=["in_mask", "roi_file","out_dir"],
output_names=["refined_mask"],
function=subtract_roi),
name='subtract_roi')
subtract_roi_node.base_dir = str(acompcor_lesionfix_wf.base_dir)
subtract_roi_node._output_dir = os.path.join(str(acompcor_lesionfix_wf.base_dir),
acc_tfm_lf.output_dir().rstrip('acc_tfm'),'subtract_roi')
subtract_roi_node.inputs.out_dir = subtract_roi_node._output_dir
# Load, clone and reconfigure the acompcor node from FMRIPREP
acompcor_old = loadpkl(os.path.join(fmriprep_ss_work_dir,
'func_preproc_{0}_wf'.format(scan_suffix),'bold_confounds_wf/acompcor/_node.pklz'))
acompcor_lf = acompcor_old.clone(name="acompcor_lf")
acompcor_lf.base_dir = str(acompcor_lesionfix_wf.base_dir)
acompcor_lf._output_dir = os.path.join(str(acompcor_lesionfix_wf.base_dir),
acompcor_lf._output_dir.split('fmriprep_wf/',1)[1])
# Load, clone and reconfigure the concat node from FMRIPREP
concat_old = loadpkl(os.path.join(fmriprep_ss_work_dir,
'func_preproc_{0}_wf'.format(scan_suffix),'bold_confounds_wf/concat/_node.pklz'))
concat_lf = concat_old.clone(name="concat_lf")
concat_lf.base_dir = str(acompcor_lesionfix_wf.base_dir)
concat_lf._output_dir = os.path.join(str(acompcor_lesionfix_wf.base_dir),
concat_lf._output_dir.split('fmriprep_wf/',1)[1])
# Load, clone and reconfigure the ds_confounds DataSink node from FMRIPREP
ds_confounds_old = loadpkl(os.path.join(fmriprep_ss_work_dir,
'func_preproc_{0}_wf'.format(scan_suffix),'func_derivatives_wf/ds_confounds/_node.pklz'))
ds_confounds_lf = ds_confounds_old.clone(name="ds_confounds_lf")
ds_confounds_lf.inputs.base_dir = os.path.join(deriv_dir,'acompcor_lesionfix/out')
ds_confounds_lf.inputs.base_directory = os.path.join(deriv_dir,'acompcor_lesionfix/out')
ds_confounds_lf._output_dir = os.path.join(str(acompcor_lesionfix_wf.base_dir),
ds_confounds_lf._output_dir.split('fmriprep_wf/',1)[1])
ds_confounds_lf.inputs.desc = 'confounds_variant-lesionfix'
# Run bidssrc node
bidssrc_lf.run()
# Connect bidssrc.outputs.roi --> acc_tfm.inputs.input_image
acc_tfm_lf.inputs.input_image = bidssrc_lf.result.outputs.roi
# Run acc_tfm node
acc_tfm_lf.run()
# Connect acc_tfm.outputs.output_image --> subtract_roi_node.inputs.roi_file
subtract_roi_node.inputs.roi_file = acc_tfm_lf.result.outputs.output_image
# Connect acompcor_lf.inputs.mask_files[0] --> subtract_roi_node.inputs.in_mask
subtract_roi_node.inputs.in_mask = acompcor_lf.inputs.mask_files[0]
# Run acc_msk node
subtract_roi_node.run()
# Connect subtract_roi_node.outputs.refined_mask --> acompcor.inputs.mask_files
acompcor_lf.inputs.mask_files = subtract_roi_node.result.outputs.refined_mask
# Run acompcor node
acompcor_lf.run()
# Connect acompcor.outputs.components_file --> concat.inputs.acompcor
concat_lf.inputs.acompcor = acompcor_lf.result.outputs.components_file
# Run concat node
concat_lf.run()
# Connect concat.outputs.confound_file --> ds_confounds.inputs.in_file
ds_confounds_lf.inputs.in_file = concat_lf.result.outputs.confounds_file
# Run ds_confounds node
ds_confounds_lf.run()
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