Segmentation Workflow#

CPAC.seg_preproc.check_if_file_is_empty(in_file)[source]#

Raise exception if regressor fie is empty.

Parameters:

in_file (nii file (string)) – regressor file

Returns:

in_file – return same file

Return type:

string

CPAC.seg_preproc.create_seg_preproc_antsJointLabel_method(wf_name='seg_preproc_templated_based')[source]#

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

Parameters:

wf_name (string) – name of the workflow

Returns:

seg_preproc_templated_based – Workflow Object for Segmentation Workflow

Return type:

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)[source]#

Returns eroded tissue segment mask

Parameters:

  • roi_mask (string) – Path to binarized segment (ROI) mask

  • erosion_prop (float) – Target volume ratio for erosion segment mask

Returns:

eroded_roi_mask – Path to eroded segment mask

Return type:

string

CPAC.seg_preproc.hardcoded_antsJointLabelFusion(anatomical_brain, anatomical_brain_mask, template_brain_list, template_segmentation_list)[source]#

run antsJointLabelFusion.sh

Parameters:

  • anatomical_brain (string (nifti file)) – Target image to be labeled.

  • anatomical_brain_mask (string (nifti file)) – Target mask image

  • template_brain_list (list) – Atlas to be warped to target image.

  • template_segmentation_list (list) – Labels corresponding to atlas.

Returns:

  • multiatlas_Intensity (string (nifti file))

  • multiatlas_Labels (string (nifti file))

CPAC.seg_preproc.mask_erosion(roi_mask=None, skullstrip_mask=None, mask_erosion_mm=None, mask_erosion_prop=None)[source]#

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_mask (string) – Path to binarized segment mask

  • skullstrip_mask (string) – Path to skull-stripped brain mask

  • mask_erosion_prop (float) – Target volume ratio for skull-stripped brain mask

Returns:

  • output_roi_mask (string) – Path to eroded segment mask

  • eroded_skullstrip_mask (string) – Path to eroded skull-stripped brain mask

CPAC.seg_preproc.pick_wm_class_0(tissue_class_files)[source]#

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

Parameters:

tissue_class_files (list (string)) – List of tissue class files

Returns:

file – Path to segment_seg_0.nii.gz is returned

Return type:

string

CPAC.seg_preproc.pick_wm_class_1(tissue_class_files)[source]#

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

Parameters:

tissue_class_files (list (string)) – List of tissue class files

Returns:

file – Path to segment_seg_1.nii.gz is returned

Return type:

string

CPAC.seg_preproc.pick_wm_class_2(tissue_class_files)[source]#

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

Parameters:

tissue_class_files (list (string)) – List of tissue class files

Returns:

file – Path to segment_seg_2.nii.gz is returned

Return type:

string

CPAC.seg_preproc.pick_wm_prob_0(probability_maps)[source]#

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

Parameters:

probability_maps (list (string)) – List of Probability Maps

Returns:

file – Path to segment_prob_0.nii.gz is returned

Return type:

string

CPAC.seg_preproc.pick_wm_prob_1(probability_maps)[source]#

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

Parameters:

probability_maps (list (string)) – List of Probability Maps

Returns:

file – Path to segment_prob_1.nii.gz is returned

Return type:

string

CPAC.seg_preproc.pick_wm_prob_2(probability_maps)[source]#

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

Parameters:

probability_maps (list (string)) – List of Probability Maps

Returns:

file – Path to segment_prob_2.nii.gz is returned

Return type:

string

CPAC.seg_preproc.process_segment_map(wf_name, use_priors, use_custom_threshold, reg_tool)[source]#

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_name (string) – Workflow Name

  • use_priors (boolean) – Whether or not to use template-space tissue priors to further refine the resulting segmentation tissue masks.

  • use_threshold (list) – Choose threshold to further refine the resulting segmentation tissue masks.

  • use_erosion (boolean) – Whether or not to erode the resulting segmentation tissue masks.

  • use_ants (boolean) – Whether or not to use ANTs or FSL for transform application.

Returns:

preproc – Workflow Object for process_segment_map Workflow

Return type:

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:

images/generated/process_segment_map.png

Detailed Graph:

images/generated/process_segment_map_detailed.png