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Merge pull request #199 from pni-lab/197-change-default-registration-…
…template Introduce ventricle mask generation workflow; Change default templates; Make templateflow template retrieval MUCH more time-efficient; Redo anat_prov, get_references and more
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,132 @@ | ||
| from PUMI.engine import QcPipeline, GroupPipeline | ||
| from PUMI.engine import NestedNode as Node | ||
| import nipype.interfaces.fsl as fsl | ||
| from nipype.interfaces.utility import Function | ||
| from PUMI.utils import get_reference | ||
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| @QcPipeline(inputspec_fields=['ventricle_mask', 'template'], | ||
| outputspec_fields=['out_file']) | ||
| def qc(wf, **kwargs): | ||
| """ | ||
| Pipeline for generating QC images for ventricle mask creation. | ||
| Inputs: | ||
| ventricle_mask (str): Path to the ventricle mask file. | ||
| template (str): Path to the template image file. | ||
| Outputs: | ||
| out_file (str): Path to the output QC image. | ||
| Parameters: | ||
| wf (Workflow): The workflow object. | ||
| kwargs (dict): Additional arguments for the workflow. | ||
| """ | ||
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| def create_image(ventricle_mask, template): | ||
| """ | ||
| Create a QC image overlaying the ventricle mask on the template. | ||
| Parameters: | ||
| ventricle_mask (str): Path to the ventricle mask file. | ||
| template (str): Path to the template image file. | ||
| Returns: | ||
| str: Path to the output QC image. | ||
| """ | ||
| from PUMI.utils import plot_roi | ||
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| _, out_file = plot_roi(roi_img=ventricle_mask, bg_img=template, cmap='winter', save_img=True) | ||
| return out_file | ||
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| plot = Node(Function(input_names=['ventricle_mask', 'template'], | ||
| output_names=['out_file'], | ||
| function=create_image), | ||
| name='plot') | ||
| wf.connect('inputspec', 'ventricle_mask', plot, 'ventricle_mask') | ||
| wf.connect('inputspec', 'template', plot, 'template') | ||
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| # Sinking | ||
| wf.connect(plot, 'out_file', 'sinker', 'qc_ventricle_mask') | ||
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| # Output | ||
| wf.connect(plot, 'out_file', 'outputspec', 'out_file') | ||
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| @GroupPipeline(inputspec_fields=['csf_probseg', 'template'], | ||
| outputspec_fields=['out_file']) | ||
| def create_ventricle_mask(wf, fallback_threshold=0, fallback_dilate_mask=0, **kwargs): | ||
| """ | ||
| Pipeline for generating a ventricle mask based on CSF probability segmentation and an atlas. | ||
| This pipeline generates a ventricle mask by thresholding the CSF probability map, | ||
| combining it with atlas-defined ventricle labels, and optionally dilating the resulting mask. | ||
| Inputs: | ||
| csf_probseg (str): Path to the CSF probability segmentation file. | ||
| template (str): Path to the template image file used for QC. | ||
| Outputs: | ||
| out_file (str): Path to the generated ventricle mask file. | ||
| Parameters: | ||
| wf (Workflow): The workflow object. | ||
| fallback_threshold (float, optional): Default threshold for the CSF probability map thresholding. | ||
| Used if not defined in the settings file (default: 0). | ||
| fallback_dilate_mask (int, optional): Default dilation value for the ventricle mask. | ||
| Used if not defined in the settings file (default: 0). | ||
| kwargs (dict): Additional arguments for the workflow. | ||
| Raises: | ||
| ValueError: If ventricle labels are not defined in the configuration file. | ||
| """ | ||
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| # Load ventricle labels from settings.ini | ||
| ventricle_labels = wf.cfg_parser.get('TEMPLATES', 'ventricle_labels', fallback='') | ||
| ventricle_labels = [int(label) for label in ventricle_labels.replace(' ', '').split(',')] | ||
| if len(ventricle_labels) == 0: | ||
| raise ValueError('You need to define ventricle labels in settings.ini!') | ||
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| # Threshold ventricle labels individually | ||
| threshold_nodes = [] | ||
| atlas = get_reference(wf, 'atlas') | ||
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| for label in ventricle_labels: | ||
| node = Node(fsl.ImageMaths(op_string=f"-thr {label} -uthr {label} -bin"), name=f'threshold_ventricle_{label}') | ||
| node.inputs.in_file = atlas | ||
| wf.add_nodes([node]) | ||
| threshold_nodes.append(node) | ||
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| # Use MultiImageMaths to combine all ventricle masks using -max | ||
| combine_ventricles_op_string = " ".join(["-add %s"] * (len(threshold_nodes) - 1)) | ||
| combine_ventricles = Node(fsl.MultiImageMaths(op_string=combine_ventricles_op_string), name='combine_ventricles') | ||
| wf.connect(threshold_nodes[0], 'out_file', combine_ventricles, 'in_file') | ||
| for n in threshold_nodes[1:]: | ||
| wf.connect(n, 'out_file', combine_ventricles, 'operand_files') | ||
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| # Dilate ventricle mask | ||
| dilate_mask_value = int(wf.cfg_parser.get('FSL', 'ImageMaths_dilate_ventricle_mask', fallback=fallback_dilate_mask)) | ||
| dilate_mask_op_string = '-dilM ' * dilate_mask_value + '-bin' | ||
| dilate_ventricle_mask = Node(fsl.ImageMaths(op_string=dilate_mask_op_string), name='dilate_ventricle_mask') | ||
| wf.connect(combine_ventricles, 'out_file', dilate_ventricle_mask, 'in_file') | ||
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| # Threshold CSF probability map | ||
| threshold = float(wf.cfg_parser.get('FSL', 'ImageMaths_ventricle_threshold', fallback=fallback_threshold)) | ||
| threshold_csf = Node(fsl.ImageMaths(op_string=f'-thr {threshold} -bin'), name='threshold_csf') | ||
| wf.connect('inputspec', 'csf_probseg', threshold_csf, 'in_file') | ||
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| # Multiply the combined ventricle mask with the CSF mask | ||
| combine_csf_ventricles = Node(fsl.MultiImageMaths(op_string='-mul %s'), name='combine_csf_ventricles') | ||
| wf.connect(threshold_csf, 'out_file', combine_csf_ventricles, 'in_file') | ||
| wf.connect(dilate_ventricle_mask, 'out_file', combine_csf_ventricles, 'operand_files') | ||
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| # QC | ||
| qc_create_ventricle_mask = qc(name='qc_create_ventricle_mask', qc_dir=wf.qc_dir) | ||
| wf.connect(combine_csf_ventricles, 'out_file', qc_create_ventricle_mask, 'ventricle_mask') | ||
| wf.connect('inputspec', 'template', qc_create_ventricle_mask, 'template') | ||
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| # Sinking | ||
| wf.connect(combine_csf_ventricles, 'out_file', 'sinker', 'create_ventricle_mask') | ||
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| # Outputspec | ||
| wf.connect(combine_csf_ventricles, 'out_file', 'outputspec', 'out_file') |
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