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added nodes to create mask of median functional image in structural s… #1144

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merged 1 commit into from
Jul 16, 2015
Merged

added nodes to create mask of median functional image in structural s… #1144

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24 changes: 22 additions & 2 deletions examples/fmri_ants_openfmri.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,6 +124,7 @@ def create_reg_workflow(name='registration'):
'transformed_files',
'transformed_mean',
'anat2target',
'mean2anat_mask'
]),
name='outputspec')

Expand Down Expand Up @@ -171,6 +172,13 @@ def create_reg_workflow(name='registration'):
register.connect(mean2anat, 'out_matrix_file',
mean2anatbbr, 'in_matrix_file')

"""
Create a mask of the median image coregistered to the anatomical image
"""

mean2anat_mask = Node(fsl.BET(mask=True), name='mean2anat_mask')
register.connect(mean2anatbbr, 'out_file', mean2anat_mask, 'in_file')

"""
Convert the BBRegister transformation to ANTS ITK format
"""
Expand Down Expand Up @@ -276,6 +284,8 @@ def create_reg_workflow(name='registration'):
register.connect(warpall, 'output_image', outputnode, 'transformed_files')
register.connect(mean2anatbbr, 'out_matrix_file',
outputnode, 'func2anat_transform')
register.connect(mean2anat_mask, 'mask_file',
outputnode, 'mean2anat_mask')
register.connect(reg, 'composite_transform',
outputnode, 'anat2target_transform')

Expand Down Expand Up @@ -333,7 +343,8 @@ def create_fs_reg_workflow(name='registration'):
'transformed_files',
'min_cost_file',
'anat2target',
'aparc'
'aparc',
'mean2anat_mask'
]),
name='outputspec')

Expand All @@ -349,7 +360,7 @@ def create_fs_reg_workflow(name='registration'):
register.connect(fssource, 'T1', convert, 'in_file')

# Coregister the median to the surface
bbregister = Node(freesurfer.BBRegister(),
bbregister = Node(freesurfer.BBRegister(registered_file=True),
name='bbregister')
bbregister.inputs.init = 'fsl'
bbregister.inputs.contrast_type = 't2'
Expand All @@ -359,6 +370,10 @@ def create_fs_reg_workflow(name='registration'):
register.connect(inputnode, 'mean_image', bbregister, 'source_file')
register.connect(inputnode, 'subjects_dir', bbregister, 'subjects_dir')

# Create a mask of the median coregistered to the anatomical image
mean2anat_mask = Node(fsl.BET(mask=True), name='mean2anat_mask')
register.connect(bbregister, 'registered_file', mean2anat_mask, 'in_file')

"""
use aparc+aseg's brain mask
"""
Expand Down Expand Up @@ -500,6 +515,8 @@ def create_fs_reg_workflow(name='registration'):
outputnode, 'out_reg_file')
register.connect(bbregister, 'min_cost_file',
outputnode, 'min_cost_file')
register.connect(mean2anat_mask, 'mask_file',
outputnode, 'mean2anat_mask')
register.connect(reg, 'composite_transform',
outputnode, 'anat2target_transform')
register.connect(merge, 'out', outputnode, 'transforms')
Expand Down Expand Up @@ -964,6 +981,8 @@ def get_subs(subject_id, conds, run_id, model_id, task_id):
subs.append(('/model%03d/task%03d_' % (model_id, task_id), '/'))
subs.append(('_bold_dtype_mcf_bet_thresh_dil', '_mask'))
subs.append(('_output_warped_image', '_anat2target'))
subs.append(('median_flirt_brain_mask', 'median_brain_mask'))
subs.append(('median_bbreg_brain_mask', 'median_brain_mask'))
return subs

subsgen = pe.Node(niu.Function(input_names=['subject_id', 'conds', 'run_id',
Expand Down Expand Up @@ -998,6 +1017,7 @@ def get_subs(subject_id, conds, run_id, model_id, task_id):
('outputspec.motion_plots',
'qa.motion.plots'),
('outputspec.mask', 'qa.mask')])])
wf.connect(registration, 'outputspec.mean2anat_mask', datasink, 'qa.mask.mean2anat')
wf.connect(art, 'norm_files', datasink, 'qa.art.@norm')
wf.connect(art, 'intensity_files', datasink, 'qa.art.@intensity')
wf.connect(art, 'outlier_files', datasink, 'qa.art.@outlier_files')
Expand Down