Segmentation Workflow

CPAC.seg_preproc.check_if_file_is_empty(in_file)

Raise exception if regressor fie is empty.

Parameters:

in_filenii file (string)

regressor file

Returns:

in_filestring

return same file

CPAC.seg_preproc.create_seg_preproc_antsJointLabel_method(wf_name='seg_preproc_templated_based')

Generate the subject’s cerebral spinal fluids, white matter and gray matter mask based on provided template, if selected to do so.

Parameters:

wf_namestring

name of the workflow

Returns:

seg_preproc_templated_basedworkflow

Workflow Object for Segmentation Workflow

Notes

Workflow Inputs:

inputspec.brain : string (existing nifti file)
    Anatomical image(without skull)

inputspec.template_brain : string (existing nifti file)
    Template anatomical image(without skull)

inputspec.template_segmentation : string (existing nifti file)
    Template segmentation image(without skull)

Workflow Outputs:

outputspec.csf_mask : string (nifti file)
    outputs CSF mask

outputspec.gm_mask : string (nifti file)
    outputs gray matter mask

outputspec.wm_mask : string (nifti file)
    outputs White Matter mask

CPAC.seg_preproc.erosion(roi_mask=None, erosion_mm=None, erosion_prop=None)

Returns eroded tissue segment mask

Parameters:

roi_maskstring

Path to binarized segment (ROI) mask

erosion_propfloat

Proportion of erosion segment mask

Returns:

eroded_roi_maskstring

Path to eroded segment mask

CPAC.seg_preproc.hardcoded_antsJointLabelFusion(anatomical_brain, anatomical_brain_mask, template_brain_list, template_segmentation_list)

run antsJointLabelFusion.sh

Parameters:

anatomical_brainstring (nifti file)

Target image to be labeled.

anatomical_brain_maskstring (nifti file)

Target mask image

template_brain_listlist

Atlas to be warped to target image.

template_segmentation_listlist

Labels corresponding to atlas.

Returns:

multiatlas_Intensitystring (nifti file)

multiatlas_Labelsstring (nifti file)

CPAC.seg_preproc.mask_erosion(roi_mask=None, skullstrip_mask=None, mask_erosion_mm=None, mask_erosion_prop=None)

Returns eroded segment mask and skull-stripped brain mask

# This functionality is adapted from poldracklab/niworkflows: # https://github.com/poldracklab/niworkflows/blob/master/niworkflows/interfaces/utils.py # https://fmriprep.readthedocs.io/ # https://poldracklab.stanford.edu/ # We are temporarily maintaining our own copy for more granular control.

Parameters:

roi_maskstring

Path to binarized segment mask

skullstrip_maskstring

Path to skull-stripped brain mask

mask_erosion_propfloat

Proportion of erosion skull-stripped brain mask

Returns:

output_roi_maskstring

Path to eroded segment mask

eroded_skullstrip_maskstring

Path to eroded skull-stripped brain mask

CPAC.seg_preproc.pick_tissue_from_labels_file(multiatlas_Labels, csf_label=[4, 14, 15, 24, 43], gm_label=[3, 42], wm_label=[2, 41])

Pick tissue mask from multiatlas labels file based off of FreeSurferColorLUT https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT or user provided label value

Parameters:

multiatlas_Labelsstring (nifti file)

csf_labellist

a list of integer label values corresponding to CSF in multiatlas file

gm_labellist

a list of integer label value corresponding to Gray Matter in multiatlas file

wm_labellist

a list of integer label value corresponding to White Matter in multiatlas file

Returns:

csf_maskstring (nifti file)

gm_maskstring (nifti file)

wm_maskstring (nifti file)

CPAC.seg_preproc.pick_wm_class_0(tissue_class_files)

Returns the csf tissue class file from the list of segmented tissue class files

Parameters:

tissue_class_fileslist (string)

List of tissue class files

Returns:

filestring

Path to segment_seg_0.nii.gz is returned

CPAC.seg_preproc.pick_wm_class_1(tissue_class_files)

Returns the gray matter tissue class file from the list of segmented tissue class files

Parameters:

tissue_class_fileslist (string)

List of tissue class files

Returns:

filestring

Path to segment_seg_1.nii.gz is returned

CPAC.seg_preproc.pick_wm_class_2(tissue_class_files)

Returns the white matter tissue class file from the list of segmented tissue class files

Parameters:

tissue_class_fileslist (string)

List of tissue class files

Returns:

filestring

Path to segment_seg_2.nii.gz is returned

CPAC.seg_preproc.pick_wm_prob_0(probability_maps)

Returns the csf probability map from the list of segmented probability maps

Parameters:

probability_mapslist (string)

List of Probability Maps

Returns:

filestring

Path to segment_prob_0.nii.gz is returned

CPAC.seg_preproc.pick_wm_prob_1(probability_maps)

Returns the gray matter probability map from the list of segmented probability maps

Parameters:

probability_mapslist (string)

List of Probability Maps

Returns:

filestring

Path to segment_prob_1.nii.gz is returned

CPAC.seg_preproc.pick_wm_prob_2(probability_maps)

Returns the white matter probability map from the list of segmented probability maps

Parameters:

probability_mapslist (string)

List of Probability Maps

Returns:

filestring

Path to segment_prob_2.nii.gz is returned

CPAC.seg_preproc.process_segment_map(wf_name, use_priors, use_custom_threshold, reg_tool)

This is a sub workflow used inside segmentation workflow to process probability maps obtained in segmentation. Steps include overlapping of the prior tissue with probability maps, thresholding and binarizing it and creating a mask that is used in further analysis.

Parameters:

wf_namestring

Workflow Name

use_priorsboolean

Whether or not to use template-space tissue priors to further refine the resulting segmentation tissue masks.

use_thresholdlist

Choose threshold to further refine the resulting segmentation tissue masks.

use_erosionboolean

Whether or not to erode the resulting segmentation tissue masks.

use_antsboolean

Whether or not to use ANTs or FSL for transform application.

Returns:

preprocworkflow

Workflow Object for process_segment_map Workflow

Notes

Source

Workflow Inputs:

inputspec.brain : string (existing nifti file)
    Anatomical image(without skull)

inputspec.standard2highres_mat : string (existing affine transformation .mat file)
    path to transformation matrix from mni space to anatomical space

inputspec.threshold : float
    threshold value

inputspec.tissue_prior : string (existing nifti file)
    path to FSL Standard Tissue prior image

inputspec.probability_tissue_map : string (nifti file)
    tissue Probability map obtained from fsl FAST

Workflow Outputs:

outputspec.segment_mni2t1 : string (nifti file)
    path to output CSF prior template(in MNI space) registered to anatomical space

outputspec.segment_combo : string (nifti file)
    path to output image containing overlap between csf probability map and segment_mni2t1

outputspec.segment_thresh : string (nifti file)
    path to output image after Thresholding segment_combo

outputspec.segment_bin : string (nifti file)
    path to output image after binarizing segment_thresh

outputspec.segment_erosion : string (nifti file)
    path to output image after eroding segment_bin

outputspec.segment_mask : string (nifti file)
    path to output image after masking segment_combo with its tissue prior in t1 space

Order of commands:

• Register tissue prior in MNI space to t1 space.

• Threshold segment probability map

• Binarize threshed segment probability map

• Erose binarized segment mask

• Generate segment mask, by applying tissue prior in t1 space to thresholded binarized segment probability map

Error

Unable to execute python code at exec.py:31:

process_segment_map() takes 4 positional arguments but 5 were given

High Level Graph:

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