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Refine PET-to-anat similarity scoring masks and smoothing #195

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Refine PET-to-anat similarity scoring masks and smoothing #195

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43 changes: 31 additions & 12 deletions petprep/workflows/pet/registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,7 @@ def init_pet_reg_wf(

"""
from nipype.interfaces.ants import MeasureImageSimilarity, Registration
from nipype.interfaces.ants.utils import ImageMath
from nipype.interfaces.freesurfer import MRIConvert, MRICoreg, RobustRegister
from nipype.interfaces.fsl import RobustFOV
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
Expand All @@ -139,7 +140,13 @@ def init_pet_reg_wf(
outputnode.inputs.registration_score = None

mask_brain = pe.Node(ApplyMask(), name='mask_brain')
mask_brain_for_score = pe.Node(ApplyMask(), name='mask_brain_for_score')
crop_anat_mask = pe.Node(MRIConvert(out_type='niigz'), name='crop_anat_mask')
erode_anat_mask = pe.Node(ImageMath(operation='ME', op2='1'), name='erode_anat_mask')
smooth_t1_for_score = pe.Node(
ImageMath(dimension=3, operation='G', op2='2.5'),
name='smooth_t1_for_score',
)
robust_fov = pe.Node(RobustFOV(output_type='NIFTI_GZ'), name='robust_fov')

if pet2anat_method == 'auto':
Expand Down Expand Up @@ -222,7 +229,11 @@ def init_pet_reg_wf(
(inputnode, crop_anat_mask, [('anat_mask', 'in_file')]),
(robust_fov, crop_anat_mask, [('out_roi', 'reslice_like')]),
(robust_fov, mask_brain, [('out_roi', 'in_file')]),
(robust_fov, mask_brain_for_score, [('out_roi', 'in_file')]),
(crop_anat_mask, mask_brain, [('out_file', 'in_mask')]),
(erode_anat_mask, mask_brain_for_score, [('output_image', 'in_mask')]),
(crop_anat_mask, erode_anat_mask, [('out_file', 'op1')]),
(mask_brain_for_score, smooth_t1_for_score, [('out_file', 'op1')]),
# ANTs branch
(inputnode, ants_coreg, [('ref_pet_brain', 'moving_image')]),
(robust_fov, ants_coreg, [('out_roi', 'fixed_image')]),
Expand All @@ -232,9 +243,9 @@ def init_pet_reg_wf(
(robust_fov, ants_warp, [('out_roi', 'reference_image')]),
(ants_convert, ants_warp, [('out_xfm', 'transforms')]),
(ants_warp, ants_score, [('output_image', 'moving_image')]),
(mask_brain, ants_score, [('out_file', 'fixed_image')]),
(crop_anat_mask, ants_score, [('out_file', 'fixed_image_mask')]),
(crop_anat_mask, ants_score, [('out_file', 'moving_image_mask')]),
(smooth_t1_for_score, ants_score, [('output_image', 'fixed_image')]),
(erode_anat_mask, ants_score, [('output_image', 'fixed_image_mask')]),
(erode_anat_mask, ants_score, [('output_image', 'moving_image_mask')]),
# FreeSurfer branch
(inputnode, fs_coreg, [('ref_pet_brain', 'source_file')]),
(mask_brain, fs_coreg, [('out_file', 'reference_file')]),
Expand All @@ -243,9 +254,9 @@ def init_pet_reg_wf(
(mask_brain, fs_warp, [('out_file', 'reference_image')]),
(fs_convert, fs_warp, [('out_xfm', 'transforms')]),
(fs_warp, fs_score, [('output_image', 'moving_image')]),
(mask_brain, fs_score, [('out_file', 'fixed_image')]),
(crop_anat_mask, fs_score, [('out_file', 'fixed_image_mask')]),
(crop_anat_mask, fs_score, [('out_file', 'moving_image_mask')]),
(smooth_t1_for_score, fs_score, [('output_image', 'fixed_image')]),
(erode_anat_mask, fs_score, [('output_image', 'fixed_image_mask')]),
(erode_anat_mask, fs_score, [('output_image', 'moving_image_mask')]),
# Selection
(ants_convert, select_best, [('out_xfm', 'xfm_ants'), ('out_inv', 'inv_ants')]),
(fs_convert, select_best, [('out_xfm', 'xfm_fs'), ('out_inv', 'inv_fs')]),
Expand Down Expand Up @@ -349,7 +360,11 @@ def init_pet_reg_wf(
# ANTs gets unmasked T1W + separate mask (not pre-masked image)
connections = [
(robust_fov, mask_brain, [('out_roi', 'in_file')]),
(robust_fov, mask_brain_for_score, [('out_roi', 'in_file')]),
(crop_anat_mask, mask_brain, [('out_file', 'in_mask')]),
(crop_anat_mask, erode_anat_mask, [('out_file', 'op1')]),
(erode_anat_mask, mask_brain_for_score, [('output_image', 'in_mask')]),
(mask_brain_for_score, smooth_t1_for_score, [('out_file', 'op1')]),
(inputnode, coreg, [('ref_pet_brain', coreg_moving)]),
(
robust_fov,
Expand All @@ -372,16 +387,20 @@ def init_pet_reg_wf(
(robust_fov, warp_for_score, [('out_roi', 'reference_image')]),
(convert_xfm, warp_for_score, [('out_xfm', 'transforms')]),
(warp_for_score, similarity, [('output_image', 'moving_image')]),
(mask_brain, similarity, [('out_file', 'fixed_image')]),
(crop_anat_mask, similarity, [('out_file', 'fixed_image_mask')]),
(crop_anat_mask, similarity, [('out_file', 'moving_image_mask')]),
(smooth_t1_for_score, similarity, [('output_image', 'fixed_image')]),
(erode_anat_mask, similarity, [('output_image', 'fixed_image_mask')]),
(erode_anat_mask, similarity, [('output_image', 'moving_image_mask')]),
(similarity, outputnode, [('similarity', 'registration_score')]),
]
else:
# mri_coreg and mri_robust_register output single transform file
connections = [
(robust_fov, mask_brain, [('out_roi', 'in_file')]),
(robust_fov, mask_brain_for_score, [('out_roi', 'in_file')]),
(crop_anat_mask, mask_brain, [('out_file', 'in_mask')]),
(crop_anat_mask, erode_anat_mask, [('out_file', 'op1')]),
(erode_anat_mask, mask_brain_for_score, [('output_image', 'in_mask')]),
(mask_brain_for_score, smooth_t1_for_score, [('out_file', 'op1')]),
(inputnode, coreg, [('ref_pet_brain', coreg_moving)]),
(mask_brain, coreg, [('out_file', coreg_target)]),
(coreg, convert_xfm, [(coreg_output, 'in_xfms')]),
Expand All @@ -397,9 +416,9 @@ def init_pet_reg_wf(
(robust_fov, warp_for_score, [('out_roi', 'reference_image')]),
(convert_xfm, warp_for_score, [('out_xfm', 'transforms')]),
(warp_for_score, similarity, [('output_image', 'moving_image')]),
(mask_brain, similarity, [('out_file', 'fixed_image')]),
(crop_anat_mask, similarity, [('out_file', 'fixed_image_mask')]),
(crop_anat_mask, similarity, [('out_file', 'moving_image_mask')]),
(smooth_t1_for_score, similarity, [('output_image', 'fixed_image')]),
(erode_anat_mask, similarity, [('output_image', 'fixed_image_mask')]),
(erode_anat_mask, similarity, [('output_image', 'moving_image_mask')]),
(similarity, outputnode, [('similarity', 'registration_score')]),
]

Expand Down