infosource.inputs.fs_subjects_dir=fs_subjects_dir
infosource.iterables=('subject_id', subjects)
# select files
templates={'realigned_epi':'preprocessed/{subject_id}/motion_correction/rest_moco_mean.nii.gz',
'anat_head':'preprocessed/{subject_id}/freesurfer_anatomy/T1_out.nii.gz',
'norm_lin':'preprocessed/{subject_id}/normalization/transform0GenericAffine.mat',
'norm_invwarp':'preprocessed/{subject_id}/normalization/transform1InverseWarp.nii.gz'
}
selectfiles = Node(nio.SelectFiles(templates,
base_directory=data_dir),
name="selectfiles")
# create epi to t1 nonlinear core workflow
nonreg_core= create_epi_t1_nonlinear_pipeline('nonreg_core')
# connect to core workflow
nonreg.connect([(infosource, selectfiles, [('subject_id', 'subject_id')]),
(infosource, nonreg_core, [('subject_id', 'inputnode.fs_subject_id'),
('fs_subjects_dir', 'inputnode.fs_subjects_dir')]),
(selectfiles, nonreg_core, [('realigned_epi', 'inputnode.realigned_epi')]),
])
if version == 'version_3' or version == 'version_4' or version == 'version_6' or version == 'version_7' or version == 'version_13' or version == 'version_14' or version == 'version_15' or version == 'version_18' or version == 'version_19':
nonreg.connect([(selectfiles, nonreg_core, [('norm_lin', 'inputnode.norm_lin'),
('norm_invwarp', 'inputnode.norm_invwarp')])])
nonreg_core.inputs.inputnode.fmap_mask = fmap_mask
def create_simulation_workflow(name):
pe_voxel_size=2.3 #has to be changed in the shiftmap scaling node directly!
unwarp_direction='y-'
# workflow
simulation = Workflow(name=name)
# inputnode
inputnode=Node(util.IdentityInterface(fields=['dwell',
'anat_head',
'distorted_epi',
'fmap_mask',
'fmap_unmasked',
'shiftmap',
'freesurfer_dir',
'freesurfer_id',
'norm_lin',
'norm_invwarp',
'nonreg_mask'
]),
name='inputnode')
# outputnode
outputnode=Node(util.IdentityInterface(fields=['lin_coreg',
'nonlin_coreg',
'fmap_coreg',
'nonlin_field',
'nonlin_field_masked',
'fmap_field_masked',
]),
name='outputnode')
# epi to t1 nonlinear core workflow
nonreg= create_epi_t1_nonlinear_pipeline('nonreg')
simulation.connect([(inputnode, nonreg, [('distorted_epi', 'inputnode.realigned_epi'),
('freesurfer_dir','inputnode.fs_subjects_dir'),
('freesurfer_id', 'inputnode.fs_subject_id')])])
simulation.connect([(inputnode, nonreg, [('norm_lin', 'inputnode.norm_lin'),
('norm_invwarp', 'inputnode.norm_invwarp'),
('nonreg_mask', 'inputnode.fmap_mask')])])
#make list from transforms
def makelist(string1, string2):
transformlist=[string1, string2]
return transformlist
transformlist = Node(interface=Function(input_names=['string1', 'string2'],output_names=['transformlist'],
function=makelist),name='transformlist')
simulation.connect([(nonreg, transformlist, [('outputnode.nonlin_epi2anat', 'string2'),
('outputnode.lin_anat2epi', 'string1')])])
# apply linear part of warp
applylin = Node(ants.ApplyTransforms(dimension=3,
output_image='lin_coreg.nii.gz',
invert_transform_flags=[True]
),
'applylin')
simulation.connect([(inputnode, applylin, [('distorted_epi', 'input_image'),
('anat_head', 'reference_image')]),
(nonreg, applylin, [('outputnode.lin_anat2epi', 'transforms')]),
(applylin, outputnode, [('output_image', 'lin_coreg')])])
# apply nonlinear warp
applynonlin = Node(ants.ApplyTransforms(dimension=3,
output_image='nonlin_coreg.nii.gz',
invert_transform_flags=[True,False]
),
'applynonlin')
simulation.connect([(inputnode, applynonlin, [('distorted_epi', 'input_image'),
('anat_head', 'reference_image')]),
(transformlist, applynonlin, [('transformlist', 'transforms')]),
(applynonlin, outputnode, [('output_image', 'nonlin_coreg')])])
# reduce ants field
def reduce_ants_field(in_file,out_file):
import nibabel as nb
import os
full_file = nb.load(in_file)
data = full_file.get_data()
reduced_file=nb.Nifti1Image(data[:,:,:,0,1], full_file.get_affine())
nb.save(reduced_file, out_file)
return os.path.abspath(out_file)
reduce_ants = Node(util.Function(input_names=['in_file', 'out_file'],
output_names=['out_file'],
function=reduce_ants_field),
name='reduce_field')
reduce_ants.inputs.out_file='nonlin_field.nii.gz'
simulation.connect([(nonreg, reduce_ants, [('outputnode.nonlin_epi2anat', 'in_file')]),
(reduce_ants, outputnode, [('out_file', 'nonlin_field')])])
# mask ants field
mask= Node(fsl.ImageMaths(op_string='-mul',
out_file='nonlin_field_masked.nii.gz'),
name='mask_fields')
simulation.connect([(inputnode, mask, [('fmap_mask', 'in_file2')]),
(reduce_ants, mask, [('out_file', 'in_file')]),
(mask, outputnode, [('out_file', 'nonlin_field_masked')])])
# mask and scale shiftmap
shiftmap = Node(fsl.MultiImageMaths(op_string='-mul %s -mul 2.3',
out_file='original_field_masked.nii.gz'),
name='shiftmap')
simulation.connect([(inputnode, shiftmap, [('shiftmap', 'in_file'),
(('fmap_mask',filename_to_list), 'operand_files')]),
(shiftmap, outputnode, [('out_file', 'fmap_field_masked')])
])
# re-unwarp using the fmap
fmap = Node(fsl.FUGUE(unwarp_direction=unwarp_direction,
smooth3d=2.0,
save_shift=True,
unwarped_file='fmap_unwarped.nii.gz',
shift_out_file='fmap_field.nii.gz'),
name='fmap')
# function to get dwelltime as float from dwell string variable
def dwell2dwelltime(dwell):
dwellstring='0.'+dwell
dwelltime=float(dwellstring)
return dwelltime
simulation.connect([(inputnode, fmap, [(('dwell', dwell2dwelltime), 'dwell_time'),
('fmap_unmasked','fmap_in_file' ),
('distorted_epi', 'in_file'),
('fmap_mask', 'mask_file')])])
# register fieldmap corrected to anatomy with bbregister
bbregister = Node(interface=fs.BBRegister(init='fsl',
contrast_type='t2',
out_fsl_file = True),
name='bbregister')
simulation.connect([(fmap, bbregister, [('unwarped_file', 'source_file')]),
(inputnode, bbregister, [('freesurfer_dir','subjects_dir'),
('freesurfer_id', 'subject_id')])])
# convert shiftmap and coreg matrix to one warpfield and apply
convertwarp = Node(fsl.utils.ConvertWarp(shiftdir=unwarp_direction,
relout=True,
out_field='fmap_fullwarp.nii.gz'),
name='convertwarp')
applywarp_fmap = Node(fsl.ApplyWarp(interp='trilinear',
relwarp=True,
out_file='fmap_coreg.nii.gz'),
name='applywarp_fmap')
simulation.connect([(inputnode, convertwarp, [('anat_head', 'reference')]),
(fmap, convertwarp, [('shift_out_file', 'shiftmap')]),
(bbregister, convertwarp, [('out_fsl_file', 'postmat')]),
(inputnode, applywarp_fmap, [('distorted_epi', 'in_file'),
('anat_head', 'ref_file')]),
(convertwarp, applywarp_fmap, [('out_field', 'field_file')]),
(applywarp_fmap, outputnode, [('out_file', 'fmap_coreg')])])
return simulation
