class T2starStudy(MriStudy, metaclass=StudyMetaClass):
desc = "T2*-weighted MRI contrast"
add_data_specs = [
# Set the magnitude to be generated from the preprocess_channels
# pipeline
FilesetSpec('magnitude',
nifti_gz_format,
'preprocess_channels_pipeline',
desc=("Generated from separate channel signals, "
"provided to 'channels'.")),
# QSM and phase processing
FilesetSpec('swi', nifti_gz_format, 'swi_pipeline'),
FilesetSpec('qsm',
nifti_gz_format,
'qsm_pipeline',
desc=("Quantitative susceptibility image resolved "
"from T2* coil images")),
# Vein analysis
FilesetSpec('composite_vein_image', nifti_gz_format, 'cv_pipeline'),
FilesetSpec('vein_mask', nifti_gz_format, 'shmrf_pipeline'),
# Templates
InputFilesetSpec('mni_template_qsm_prior',
STD_IMAGE_FORMATS,
frequency='per_study',
default=LocalReferenceData('QSMPrior',
nifti_gz_format)),
InputFilesetSpec('mni_template_swi_prior',
STD_IMAGE_FORMATS,
frequency='per_study',
default=LocalReferenceData('SWIPrior',
nifti_gz_format)),
InputFilesetSpec('mni_template_atlas_prior',
STD_IMAGE_FORMATS,
frequency='per_study',
default=LocalReferenceData('VeinFrequencyPrior',
nifti_gz_format)),
InputFilesetSpec('mni_template_vein_atlas',
STD_IMAGE_FORMATS,
frequency='per_study',
default=LocalReferenceData('VeinFrequencyMap',
nifti_gz_format))
]
add_param_specs = [
SwitchSpec('qsm_dual_echo', False),
ParamSpec('qsm_echo',
1,
desc=("Which echo (by index starting at 1) to use when "
"using single echo")),
ParamSpec('qsm_padding', [12, 12, 12]),
ParamSpec('qsm_mask_dialation', [11, 11, 11]),
ParamSpec('qsm_erosion_size', 10),
SwitchSpec('bet_robust', False),
SwitchSpec('bet_robust', False),
ParamSpec('bet_f_threshold', 0.1),
ParamSpec('bet_g_threshold', 0.0)
]
def preprocess_channels_pipeline(self, **name_maps):
pipeline = super().preprocess_channels_pipeline(**name_maps)
# Connect combined first echo output to the magnitude data spec
pipeline.connect_output('magnitude', pipeline.node('to_polar'),
'first_echo', nifti_gz_format)
return pipeline
def qsm_pipeline(self, **name_maps):
"""
Process dual echo data for QSM (TE=[7.38, 22.14])
NB: Default values come from the STI-Suite
"""
pipeline = self.new_pipeline(
name='qsm_pipeline',
name_maps=name_maps,
desc="Resolve QSM from t2star coils",
citations=[sti_cites, fsl_cite, matlab_cite])
erosion = pipeline.add(
'mask_erosion',
fsl.ErodeImage(kernel_shape='sphere',
kernel_size=self.parameter('qsm_erosion_size'),
output_type='NIFTI'),
inputs={'in_file': ('brain_mask', nifti_gz_format)},
requirements=[fsl_req.v('5.0.8')],
wall_time=15,
mem_gb=12)
# If we have multiple echoes we can combine the phase images from
# each channel into a single image. Otherwise for single echo sequences
# we need to perform QSM on each coil separately and then combine
# afterwards.
if self.branch('qsm_dual_echo'):
# Combine channels to produce phase and magnitude images
channel_combine = pipeline.add(
'channel_combine',
HIPCombineChannels(),
inputs={
'magnitudes_dir': ('mag_channels', multi_nifti_gz_format),
'phases_dir': ('phase_channels', multi_nifti_gz_format)
})
# Unwrap phase using Laplacian unwrapping
unwrap = pipeline.add(
'unwrap',
UnwrapPhase(padsize=self.parameter('qsm_padding')),
inputs={
'voxelsize': ('voxel_sizes', float),
'in_file': (channel_combine, 'phase')
},
requirements=[matlab_req.v('r2017a'),
sti_req.v(2.2)])
# Remove background noise
vsharp = pipeline.add(
"vsharp",
VSharp(mask_manip="imerode({}>0, ball(5))"),
inputs={
'voxelsize': ('voxel_sizes', float),
'in_file': (unwrap, 'out_file'),
'mask': (erosion, 'out_file')
},
requirements=[matlab_req.v('r2017a'),
sti_req.v(2.2)])
# Run QSM iLSQR
pipeline.add('qsmrecon',
QSMiLSQR(mask_manip="{}>0",
padsize=self.parameter('qsm_padding')),
inputs={
'voxelsize': ('voxel_sizes', float),
'te': ('echo_times', float),
'B0': ('main_field_strength', float),
'H': ('main_field_orient', float),
'in_file': (vsharp, 'out_file'),
'mask': (vsharp, 'new_mask')
},
outputs={'qsm': ('qsm', nifti_format)},
requirements=[matlab_req.v('r2017a'),
sti_req.v(2.2)])
else:
# Dialate eroded mask
dialate = pipeline.add(
'dialate',
DialateMask(dialation=self.parameter('qsm_mask_dialation')),
inputs={'in_file': (erosion, 'out_file')},
requirements=[matlab_req.v('r2017a')])
# List files for the phases of separate channel
list_phases = pipeline.add(
'list_phases',
ListDir(sort_key=coil_sort_key,
filter=CoilEchoFilter(self.parameter('qsm_echo'))),
inputs={
'directory': ('phase_channels', multi_nifti_gz_format)
})
# List files for the phases of separate channel
list_mags = pipeline.add(
'list_mags',
ListDir(sort_key=coil_sort_key,
filter=CoilEchoFilter(self.parameter('qsm_echo'))),
inputs={'directory': ('mag_channels', multi_nifti_gz_format)})
# Generate coil specific masks
mask_coils = pipeline.add(
'mask_coils',
MaskCoils(dialation=self.parameter('qsm_mask_dialation')),
inputs={
'masks': (list_mags, 'files'),
'whole_brain_mask': (dialate, 'out_file')
},
requirements=[matlab_req.v('r2017a')])
# Unwrap phase
unwrap = pipeline.add(
'unwrap',
BatchUnwrapPhase(padsize=self.parameter('qsm_padding')),
inputs={
'voxelsize': ('voxel_sizes', float),
'in_file': (list_phases, 'files')
},
requirements=[matlab_req.v('r2017a'),
sti_req.v(2.2)])
# Background phase removal
vsharp = pipeline.add(
"vsharp",
BatchVSharp(mask_manip='{}>0'),
inputs={
'voxelsize': ('voxel_sizes', float),
'mask': (mask_coils, 'out_files'),
'in_file': (unwrap, 'out_file')
},
requirements=[matlab_req.v('r2017a'),
sti_req.v(2.2)])
first_echo_time = pipeline.add(
'first_echo',
Select(index=0),
inputs={'inlist': ('echo_times', float)})
# Perform channel-wise QSM
coil_qsm = pipeline.add(
'coil_qsmrecon',
BatchQSMiLSQR(mask_manip="{}>0",
padsize=self.parameter('qsm_padding')),
inputs={
'voxelsize': ('voxel_sizes', float),
'B0': ('main_field_strength', float),
'H': ('main_field_orient', float),
'in_file': (vsharp, 'out_file'),
'mask': (vsharp, 'new_mask'),
'te': (first_echo_time, 'out')
},
requirements=[matlab_req.v('r2017a'),
sti_req.v(2.2)],
wall_time=45) # FIXME: Should be dependent on number of coils
# Combine channel QSM by taking the median coil value
pipeline.add('combine_qsm',
MedianInMasks(),
inputs={
'channels': (coil_qsm, 'out_file'),
'channel_masks': (vsharp, 'new_mask'),
'whole_brain_mask': (dialate, 'out_file')
},
outputs={'qsm': ('out_file', nifti_format)},
requirements=[matlab_req.v('r2017a')])
return pipeline
def swi_pipeline(self, **name_maps):
raise NotImplementedError
pipeline = self.new_pipeline(
name='swi',
name_maps=name_maps,
desc=("Calculate susceptibility-weighted image from magnitude and "
"phase"))
return pipeline
def cv_pipeline(self, **name_maps):
pipeline = self.new_pipeline(name='cv_pipeline',
name_maps=name_maps,
desc="Compute Composite Vein Image",
citations=[fsl_cite, matlab_cite])
# Interpolate priors and atlas
merge_trans = pipeline.add('merge_transforms',
Merge(3),
inputs={
'in1':
('coreg_ants_mat', text_matrix_format),
'in2': ('coreg_to_tmpl_ants_mat',
text_matrix_format),
'in3': ('coreg_to_tmpl_ants_warp',
nifti_gz_format)
})
apply_trans_q = pipeline.add(
'ApplyTransform_Q_Prior',
ants.resampling.ApplyTransforms(
interpolation='Linear',
input_image_type=3,
invert_transform_flags=[True, True, False]),
inputs={
'input_image': ('mni_template_qsm_prior', nifti_gz_format),
'reference_image': ('qsm', nifti_gz_format),
'transforms': (merge_trans, 'out')
},
requirements=[ants_req.v('1.9')],
mem_gb=16,
wall_time=30)
apply_trans_s = pipeline.add(
'ApplyTransform_S_Prior',
ants.resampling.ApplyTransforms(
interpolation='Linear',
input_image_type=3,
invert_transform_flags=[True, True, False]),
inputs={
'input_image': ('mni_template_swi_prior', nifti_gz_format),
'reference_image': ('qsm', nifti_gz_format),
'transforms': (merge_trans, 'out')
},
requirements=[ants_req.v('1.9')],
mem_gb=16,
wall_time=30)
apply_trans_a = pipeline.add(
'ApplyTransform_A_Prior',
ants.resampling.ApplyTransforms(
interpolation='Linear',
input_image_type=3,
invert_transform_flags=[True, True, False],
),
inputs={
'reference_image': ('qsm', nifti_gz_format),
'input_image': ('mni_template_atlas_prior', nifti_gz_format),
'transforms': (merge_trans, 'out')
},
requirements=[ants_req.v('1.9')],
mem_gb=16,
wall_time=30)
apply_trans_v = pipeline.add(
'ApplyTransform_V_Atlas',
ants.resampling.ApplyTransforms(
interpolation='Linear',
input_image_type=3,
invert_transform_flags=[True, True, False]),
inputs={
'input_image': ('mni_template_vein_atlas', nifti_gz_format),
'reference_image': ('qsm', nifti_gz_format),
'transforms': (merge_trans, 'out')
},
requirements=[ants_req.v('1.9')],
mem_gb=16,
wall_time=30)
# Run CV code
pipeline.add(
'cv_image',
interface=CompositeVeinImage(),
inputs={
'mask': ('brain_mask', nifti_format),
'qsm': ('qsm', nifti_format),
'swi': ('swi', nifti_format),
'q_prior': (apply_trans_q, 'output_image'),
's_prior': (apply_trans_s, 'output_image'),
'a_prior': (apply_trans_a, 'output_image'),
'vein_atlas': (apply_trans_v, 'output_image')
},
outputs={'composite_vein_image': ('out_file', nifti_format)},
requirements=[matlab_req.v('R2015a')],
wall_time=300,
mem_gb=24)
return pipeline
def shmrf_pipeline(self, **name_maps):
pipeline = self.new_pipeline(name='shmrf_pipeline',
name_maps=name_maps,
desc="Compute Vein Mask using ShMRF",
citations=[fsl_cite, matlab_cite])
# Run ShMRF code
pipeline.add('shmrf',
ShMRF(),
inputs={
'in_file': ('composite_vein_image', nifti_format),
'mask': ('brain_mask', nifti_format)
},
outputs={'vein_mask': ('out_file', nifti_format)},
requirements=[matlab_req.v('R2015a')],
wall_time=30,
mem_gb=16)
return pipeline
def cet_T2s(self, **options):
pipeline = self.new_pipeline(
name='CET_T2s',
desc=("Construct cerebellum mask using SUIT template"),
default_options={
'SUIT_mask': self._lookup_template_mask_path('SUIT')
},
citations=[fsl_cite],
options=options)
# Initially use MNI space to warp SUIT mask into T2s space
merge_trans = pipeline.add(
'merge_transforms',
Merge(3),
inputs={
'in3': (self._lookup_nl_tfm_inv_name('SUIT'), nifti_gz_format),
'in2': (self._lookup_l_tfm_to_name('SUIT'), nifti_gz_format),
'in1': ('T2s_to_T1_mat', text_matrix_format)
})
apply_trans = pipeline.add(
'ApplyTransform',
ants.resampling.ApplyTransforms(
interpolation='NearestNeighbor',
input_image_type=3,
invert_transform_flags=[True, True, False],
input_image=pipeline.option('SUIT_mask')),
inputs={
'transforms': (merge_trans, 'out'),
'reference_image': ('betted_T2s', nifti_gz_format)
},
outputs={'cetted_T2s_mask': ('output_image', nifti_gz_format)},
requirements=[ants_req.v('1.9')],
mem_gb=16,
wall_time=120)
# Combine masks
maths1 = pipeline.add('combine_masks',
fsl.utils.ImageMaths(suffix='_optiBET_masks',
op_string='-mas',
output_type='NIFTI_GZ'),
inputs={
'in_file':
('betted_T2s_mask', nifti_gz_format),
'in_file2': (apply_trans, 'output_image')
},
requirements=[fsl_req.v('5.0.8')],
mem_gb=16,
wall_time=5)
# Mask out t2s image
pipeline.add('mask_t2s',
fsl.utils.ImageMaths(suffix='_optiBET_cerebellum',
op_string='-mas',
output_type='NIFTI_GZ'),
inputs={
'in_file': ('betted_T2s', nifti_gz_format),
'in_file2': (maths1, 'output_image')
},
outputs={'cetted_T2s': ('out_file', nifti_gz_format)},
requirements=[fsl_req.v('5.0.8')],
mem_gb=16,
wall_time=5)
pipeline.add(
'mask_t2s_last_echo',
fsl.utils.ImageMaths(suffix='_optiBET_cerebellum',
op_string='-mas',
output_type='NIFTI_GZ'),
inputs={
'in_file': ('betted_T2s_last_echo', nifti_gz_format),
'in_file2': (maths1, 'output_image')
},
outputs={'cetted_T2s_last_echo': ('out_file', nifti_gz_format)},
requirements=[fsl_req.v('5.0.8')],
mem_gb=16,
wall_time=5)
return pipeline
def bet_T2s(self, **options):
pipeline = self.new_pipeline(name='BET_T2s',
desc=("python implementation of BET"),
default_options={},
citations=[fsl_cite],
options=options)
bet = pipeline.add('bet',
fsl.BET(frac=0.1, mask=True,
output_type='NIFTI_GZ'),
inputs={'in_file': ('t2s', nifti_gz_format)},
outputs={
'betted_T2s': ('out_file', nifti_gz_format),
'betted_T2s_mask':
('mask_file', nifti_gz_format)
},
requirements=[fsl_req.v('5.0.8')],
mem_gb=8,
wall_time=45)
pipeline.add(
'mask',
fsl.utils.ImageMaths(suffix='_BET_brain',
op_string='-mas',
output_type='NIFTI_GZ'),
inputs={
'in_file': ('t2s_last_echo', nifti_gz_format),
'in_file2': (bet, 'mask_file')
},
outputs={'betted_T2s_last_echo': ('out_file', nifti_gz_format)},
requirements=[fsl_req.v('5.0.8')],
mem_gb=16,
wall_time=5)
return pipeline
class T1Study(T2Study, metaclass=StudyMetaClass):
desc = "T1-weighted MRI contrast"
add_data_specs = [
FilesetSpec('fs_recon_all', zip_format, 'freesurfer_pipeline'),
InputFilesetSpec(
't2_coreg',
STD_IMAGE_FORMATS,
optional=True,
desc=("A coregistered T2 image to use in freesurfer to help "
"distinguish the peel surface")),
# Templates
InputFilesetSpec('suit_mask',
STD_IMAGE_FORMATS,
frequency='per_study',
default=LocalReferenceData('SUIT', nifti_format)),
FilesetSpec('five_tissue_type',
mrtrix_image_format,
'gen_5tt_pipeline',
desc=("A segmentation image taken from freesurfer output "
"and simplified into 5 tissue types. Used in ACT "
"streamlines tractography"))
] + [
FilesetSpec('aparc_stats_{}_{}_table'.format(h, m),
text_format,
'aparc_stats_table_pipeline',
frequency='per_visit',
pipeline_args={
'hemisphere': h,
'measure': m
},
desc=("Table of {} of {} per parcellated segment".format(
m, h.upper())))
for h, m in itertools.product(
('lh', 'rh'), ('volume', 'thickness', 'thicknessstd', 'meancurv',
'gauscurv', 'foldind', 'curvind'))
]
add_param_specs = [
# MriStudy.param_spec('bet_method').with_new_choices(default='opti_bet'),
SwitchSpec('bet_robust', False),
SwitchSpec('bet_reduce_bias', True),
SwitchSpec('aparc_atlas',
'desikan-killiany',
choices=('desikan-killiany', 'destrieux', 'DKT')),
ParamSpec('bet_f_threshold', 0.1),
ParamSpec('bet_g_threshold', 0.0)
]
default_bids_inputs = [
BidsInputs(spec_name='magnitude',
type='T1w',
valid_formats=(nifti_gz_x_format, nifti_gz_format))
]
def freesurfer_pipeline(self, **name_maps):
"""
Segments grey matter, white matter and CSF from T1 images using
SPM "NewSegment" function.
NB: Default values come from the W2MHS toolbox
"""
pipeline = self.new_pipeline(name='segmentation',
name_maps=name_maps,
desc="Segment white/grey matter and csf",
citations=copy(freesurfer_cites))
# FS ReconAll node
recon_all = pipeline.add(
'recon_all',
interface=ReconAll(directive='all',
openmp=self.processor.num_processes),
inputs={'T1_files': ('mag_preproc', nifti_gz_format)},
requirements=[freesurfer_req.v('5.3')],
wall_time=2000)
if self.provided('t2_coreg'):
pipeline.connect_input('t2_coreg', recon_all, 'T2_file',
nifti_gz_format)
recon_all.inputs.use_T2 = True
# Wrapper around os.path.join
pipeline.add('join',
JoinPath(),
inputs={
'dirname': (recon_all, 'subjects_dir'),
'filename': (recon_all, 'subject_id')
},
outputs={'fs_recon_all': ('path', directory_format)})
return pipeline
def segmentation_pipeline(self, **name_maps):
pipeline = super(T1Study, self).segmentation_pipeline(img_type=1,
**name_maps)
return pipeline
def gen_5tt_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='gen5tt',
name_maps=name_maps,
desc=("Generate 5-tissue-type image used for Anatomically-"
"Constrained Tractography (ACT)"))
aseg_path = pipeline.add(
'aseg_path',
AppendPath(sub_paths=['mri', 'aseg.mgz']),
inputs={'base_path': ('fs_recon_all', directory_format)})
pipeline.add(
'gen5tt',
mrtrix3.Generate5tt(algorithm='freesurfer', out_file='5tt.mif'),
inputs={'in_file': (aseg_path, 'out_path')},
outputs={'five_tissue_type': ('out_file', mrtrix_image_format)},
requirements=[mrtrix_req.v('3.0rc3'),
freesurfer_req.v('6.0')])
return pipeline
def aparc_stats_table_pipeline(self, measure, hemisphere, **name_maps):
pipeline = self.new_pipeline(
name='aparc_stats_{}_{}'.format(hemisphere, measure),
name_maps=name_maps,
desc=("Extract statistics from freesurfer outputs"))
copy_to_dir = pipeline.add('copy_to_subjects_dir',
CopyToDir(),
inputs={
'in_files':
('fs_recon_all', directory_format),
'file_names': (self.SUBJECT_ID, int)
},
joinsource=self.SUBJECT_ID,
joinfield=['in_files', 'file_names'])
if self.branch('aparc_atlas', 'desikan-killiany'):
parc = 'aparc'
elif self.branch('aparc_atlas', 'destrieux'):
parc = 'aparc.a2009s'
elif self.branch('aparc_atlas', 'DKT'):
parc = 'aparc.DKTatlas40'
else:
self.unhandled_branch('aparc_atlas')
pipeline.add('aparc_stats',
AparcStats(measure=measure,
hemisphere=hemisphere,
parc=parc),
inputs={
'subjects_dir': (copy_to_dir, 'out_dir'),
'subjects': (copy_to_dir, 'file_names')
},
outputs={
'aparc_stats_{}_{}_table'.format(hemisphere, measure):
('tablefile', text_format)
},
requirements=[freesurfer_req.v('5.3')])
return pipeline
def bet_T1(self, **name_maps):
pipeline = self.new_pipeline(
name='BET_T1',
name_maps=name_maps,
desc=("Brain extraction pipeline using FSL's BET"),
citations=[fsl_cite])
bias = pipeline.add('n4_bias_correction',
ants.N4BiasFieldCorrection(),
inputs={'input_image': ('t1', nifti_gz_format)},
requirements=[ants_req.v('1.9')],
wall_time=60,
mem_gb=12)
pipeline.add('bet',
fsl.BET(frac=0.15,
reduce_bias=True,
output_type='NIFTI_GZ'),
inputs={'in_file': (bias, 'output_image')},
outputs={
'betted_T1': ('out_file', nifti_gz_format),
'betted_T1_mask': ('mask_file', nifti_gz_format)
},
requirements=[fsl_req.v('5.0.8')],
mem_gb=8,
wall_time=45)
return pipeline
def cet_T1(self, **name_maps):
pipeline = self.new_pipeline(
name='CET_T1',
name_maps=name_maps,
desc=("Construct cerebellum mask using SUIT template"),
citations=[fsl_cite])
# FIXME: Should convert to inputs
nl = self._lookup_nl_tfm_inv_name('MNI')
linear = self._lookup_l_tfm_to_name('MNI')
# Initially use MNI space to warp SUIT into T1 and threshold to mask
merge_trans = pipeline.add('merge_transforms',
Merge(2),
inputs={
'in2': (nl, nifti_gz_format),
'in1': (linear, nifti_gz_format)
})
apply_trans = pipeline.add('ApplyTransform',
ants.resampling.ApplyTransforms(
interpolation='NearestNeighbor',
input_image_type=3,
invert_transform_flags=[True, False]),
inputs={
'reference_image':
('betted_T1', nifti_gz_format),
'input_image':
('suit_mask', nifti_gz_format),
'transforms': (merge_trans, 'out')
},
requirements=[ants_req.v('1.9')],
mem_gb=16,
wall_time=120)
pipeline.add('maths2',
fsl.utils.ImageMaths(suffix='_optiBET_cerebellum',
op_string='-mas'),
inputs={
'in_file': ('betted_T1', nifti_gz_format),
'in_file2': (apply_trans, 'output_image')
},
outputs={
'cetted_T1': ('out_file', nifti_gz_format),
'cetted_T1_mask': ('output_image', nifti_gz_format)
},
requirements=[fsl_req.v('5.0.8')],
mem_gb=16,
wall_time=5)
return pipeline
class MotionDetectionMixin(MultiStudy, metaclass=MultiStudyMetaClass):
# add_substudy_specs = [
# SubStudySpec('pet_mc', PetStudy)]
add_data_specs = [
InputFilesetSpec('pet_data_dir', directory_format, optional=True),
InputFilesetSpec('pet_data_reconstructed',
directory_format,
optional=True),
InputFilesetSpec('struct2align', nifti_gz_format, optional=True),
InputFilesetSpec('umap', dicom_format, optional=True),
FilesetSpec('pet_data_prepared', directory_format,
'prepare_pet_pipeline'),
FilesetSpec('static_motion_correction_results', directory_format,
'motion_correction_pipeline'),
FilesetSpec('dynamic_motion_correction_results', directory_format,
'motion_correction_pipeline'),
FilesetSpec('mean_displacement', text_format,
'mean_displacement_pipeline'),
FilesetSpec('mean_displacement_rc', text_format,
'mean_displacement_pipeline'),
FilesetSpec('mean_displacement_consecutive', text_format,
'mean_displacement_pipeline'),
FilesetSpec('mats4average', text_format, 'mean_displacement_pipeline'),
FilesetSpec('start_times', text_format, 'mean_displacement_pipeline'),
FilesetSpec('motion_par_rc', text_format,
'mean_displacement_pipeline'),
FilesetSpec('motion_par', text_format, 'mean_displacement_pipeline'),
FilesetSpec('offset_indexes', text_format,
'mean_displacement_pipeline'),
FilesetSpec('severe_motion_detection_report', text_format,
'mean_displacement_pipeline'),
FilesetSpec('frame_start_times', text_format,
'motion_framing_pipeline'),
FilesetSpec('frame_vol_numbers', text_format,
'motion_framing_pipeline'),
FilesetSpec('timestamps', directory_format, 'motion_framing_pipeline'),
FilesetSpec('mean_displacement_plot', png_format,
'plot_mean_displacement_pipeline'),
FilesetSpec('rotation_plot', png_format,
'plot_mean_displacement_pipeline'),
FilesetSpec('translation_plot', png_format,
'plot_mean_displacement_pipeline'),
FilesetSpec('average_mats', directory_format,
'frame_mean_transformation_mats_pipeline'),
FilesetSpec('correction_factors', text_format,
'pet_correction_factors_pipeline'),
FilesetSpec('umaps_align2ref', directory_format,
'umap_realignment_pipeline'),
FilesetSpec('umap_aligned_dicoms', directory_format,
'nifti2dcm_conversion_pipeline'),
FilesetSpec('motion_detection_output', directory_format,
'gather_outputs_pipeline'),
FilesetSpec('moco_series', directory_format,
'create_moco_series_pipeline'),
FilesetSpec('fixed_binning_mats', directory_format,
'fixed_binning_pipeline'),
FieldSpec('pet_duration', int, 'pet_header_extraction_pipeline'),
FieldSpec('pet_end_time', str, 'pet_header_extraction_pipeline'),
FieldSpec('pet_start_time', str, 'pet_header_extraction_pipeline')
]
add_param_specs = [
ParamSpec('framing_th', 2.0),
ParamSpec('framing_temporal_th', 30.0),
ParamSpec('framing_duration', 0),
ParamSpec('md_framing', True),
ParamSpec('align_pct', False),
ParamSpec('align_fixed_binning', False),
ParamSpec('moco_template',
os.path.join(reference_path, 'moco_template.IMA')),
ParamSpec('PET_template_MNI',
os.path.join(template_path, 'PET_template_MNI.nii.gz')),
ParamSpec('fixed_binning_n_frames', 0),
ParamSpec('pet_offset', 0),
ParamSpec('fixed_binning_bin_len', 60),
ParamSpec('crop_xmin', 100),
ParamSpec('crop_xsize', 130),
ParamSpec('crop_ymin', 100),
ParamSpec('crop_ysize', 130),
ParamSpec('crop_zmin', 20),
ParamSpec('crop_zsize', 100),
ParamSpec('PET2MNI_reg', False),
ParamSpec('dynamic_pet_mc', False)
]
def mean_displacement_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='mean_displacement_calculation',
desc=("Calculate the mean displacement between each motion"
" matrix and a reference."),
citations=[fsl_cite],
name_maps=name_maps)
motion_mats_in = {}
tr_in = {}
start_time_in = {}
real_duration_in = {}
merge_index = 1
input_names = []
for spec in self.substudy_specs():
try:
spec.map('motion_mats')
except ArcanaNameError:
pass # Sub study doesn't have motion mats spec
else:
k = 'in{}'.format(merge_index)
motion_mats_in[k] = (spec.map('motion_mats'),
motion_mats_format)
tr_in[k] = (spec.map('tr'), float)
start_time_in[k] = (spec.map('start_time'), float)
real_duration_in[k] = (spec.map('real_duration'), float)
input_names.append(
self.spec(spec.map(
spec.study_class.primary_scan_name)).pattern)
merge_index += 1
merge_motion_mats = pipeline.add('merge_motion_mats',
Merge(len(motion_mats_in)),
inputs=motion_mats_in)
merge_tr = pipeline.add('merge_tr', Merge(len(tr_in)), inputs=tr_in)
merge_start_time = pipeline.add('merge_start_time',
Merge(len(start_time_in)),
inputs=start_time_in)
merge_real_duration = pipeline.add('merge_real_duration',
Merge(len(real_duration_in)),
inputs=real_duration_in)
pipeline.add(
'scan_time_info',
MeanDisplacementCalculation(input_names=input_names),
inputs={
'motion_mats': (merge_motion_mats, 'out'),
'trs': (merge_tr, 'out'),
'start_times': (merge_start_time, 'out'),
'real_durations': (merge_real_duration, 'out'),
'reference': ('ref_brain', nifti_gz_format)
},
outputs={
'mean_displacement': ('mean_displacement', text_format),
'mean_displacement_rc': ('mean_displacement_rc', text_format),
'mean_displacement_consecutive':
('mean_displacement_consecutive', text_format),
'start_times': ('start_times', text_format),
'motion_par_rc': ('motion_parameters_rc', text_format),
'motion_par': ('motion_parameters', text_format),
'offset_indexes': ('offset_indexes', text_format),
'mats4average': ('mats4average', text_format),
'severe_motion_detection_report':
('corrupted_volumes', text_format)
})
return pipeline
def motion_framing_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='motion_framing',
desc=("Calculate when the head movement exceeded a "
"predefined threshold (default 2mm)."),
citations=[fsl_cite],
name_maps=name_maps)
framing = pipeline.add(
'motion_framing',
MotionFraming(
motion_threshold=self.parameter('framing_th'),
temporal_threshold=self.parameter('framing_temporal_th'),
pet_offset=self.parameter('pet_offset'),
pet_duration=self.parameter('framing_duration')),
inputs={
'mean_displacement': ('mean_displacement', text_format),
'mean_displacement_consec':
('mean_displacement_consecutive', text_format),
'start_times': ('start_times', text_format)
},
outputs={
'frame_start_times': ('frame_start_times', text_format),
'frame_vol_numbers': ('frame_vol_numbers', text_format),
'timestamps': ('timestamps_dir', directory_format)
})
if 'pet_data_dir' in self.input_names:
pipeline.connect_input('pet_start_time', framing, 'pet_start_time')
pipeline.connect_input('pet_end_time', framing, 'pet_end_time')
return pipeline
def plot_mean_displacement_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='plot_mean_displacement',
desc=("Plot the mean displacement real clock"),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
'plot_md',
PlotMeanDisplacementRC(framing=self.parameter('md_framing')),
inputs={
'mean_disp_rc': ('mean_displacement_rc', text_format),
'false_indexes': ('offset_indexes', text_format),
'frame_start_times': ('frame_start_times', text_format),
'motion_par_rc': ('motion_par_rc', text_format)
},
outputs={
'mean_displacement_plot': ('mean_disp_plot', png_format),
'rotation_plot': ('rot_plot', png_format),
'translation_plot': ('trans_plot', png_format)
})
return pipeline
def frame_mean_transformation_mats_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='frame_mean_transformation_mats',
desc=("Average all the transformation mats within each "
"detected frame."),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
'mats_averaging',
AffineMatAveraging(),
inputs={
'frame_vol_numbers': ('frame_vol_numbers', text_format),
'all_mats4average': ('mats4average', text_format)
},
outputs={'average_mats': ('average_mats', directory_format)})
return pipeline
def fixed_binning_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='fixed_binning',
desc=("Pipeline to generate average motion matrices for "
"each bin in a dynamic PET reconstruction experiment."
"This will be the input for the dynamic motion correction."),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
'fixed_binning',
FixedBinning(n_frames=self.parameter('fixed_binning_n_frames'),
pet_offset=self.parameter('pet_offset'),
bin_len=self.parameter('fixed_binning_bin_len')),
inputs={
'start_times': ('start_times', text_format),
'pet_start_time': ('pet_start_time', str),
'pet_duration': ('pet_duration', int),
'motion_mats': ('mats4average', text_format)
},
outputs={
'fixed_binning_mats': ('average_bin_mats', directory_format)
})
return pipeline
def pet_correction_factors_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='pet_correction_factors',
desc=("Pipeline to calculate the correction factors to "
"account for frame duration when averaging the PET "
"frames to create the static PET image"),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
'pet_corr_factors',
PetCorrectionFactor(),
inputs={'timestamps': ('timestamps', directory_format)},
outputs={'correction_factors': ('corr_factors', text_format)})
return pipeline
def nifti2dcm_conversion_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='conversion_to_dicom',
desc=("Conversing aligned umap from nifti to dicom format - "
"parallel implementation"),
citations=(),
name_maps=name_maps)
list_niftis = pipeline.add(
'list_niftis',
ListDir(),
inputs={'directory': ('umaps_align2ref', directory_format)})
reorient_niftis = pipeline.add('reorient_niftis',
ReorientUmap(),
inputs={
'niftis': (list_niftis, 'files'),
'umap': ('umap', dicom_format)
},
requirements=[mrtrix_req.v('3.0rc3')])
list_dicoms = pipeline.add(
'list_dicoms',
ListDir(sort_key=dicom_fname_sort_key),
inputs={'directory': ('umap', dicom_format)})
nii2dicom = pipeline.add(
'nii2dicom',
Nii2Dicom(
# extension='Frame', # nii2dicom parameter
),
inputs={'reference_dicom': (list_dicoms, 'files')},
outputs={'in_file': (reorient_niftis, 'reoriented_umaps')},
iterfield=['in_file'],
wall_time=20)
pipeline.add(
'copy2dir',
CopyToDir(extension='Frame'),
inputs={'in_files': (nii2dicom, 'out_file')},
outputs={'umap_aligned_dicoms': ('out_dir', directory_format)})
return pipeline
def umap_realignment_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='umap_realignment',
desc=("Pipeline to align the original umap (if provided)"
"to match the head position in each frame and improve the "
"static PET image quality."),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
'umap2ref_alignment',
UmapAlign2Reference(pct=self.parameter('align_pct')),
inputs={
'ute_regmat': ('umap_ref_coreg_matrix', text_matrix_format),
'ute_qform_mat': ('umap_ref_qform_mat', text_matrix_format),
'average_mats': ('average_mats', directory_format),
'umap': ('umap', nifti_gz_format)
},
outputs={'umaps_align2ref': ('umaps_align2ref', directory_format)},
requirements=[fsl_req.v('5.0.9')])
return pipeline
def create_moco_series_pipeline(self, **name_maps):
"""This pipeline is probably wrong as we still do not know how to
import back the new moco series into the scanner. This was just a first
attempt.
"""
pipeline = self.new_pipeline(
name='create_moco_series',
desc=("Pipeline to generate a moco_series that can be then "
"imported back in the scanner and used to correct the"
" pet data"),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
'create_moco_series',
CreateMocoSeries(moco_template=self.parameter('moco_template')),
inputs={
'start_times': ('start_times', text_format),
'motion_par': ('motion_par', text_format)
},
outputs={'moco_series': ('modified_moco', directory_format)})
return pipeline
def gather_outputs_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='gather_motion_detection_outputs',
desc=("Pipeline to gather together all the outputs from "
"the motion detection pipeline."),
citations=[fsl_cite],
name_maps=name_maps)
merge_inputs = pipeline.add(
'merge_inputs',
Merge(5),
inputs={
'in1': ('mean_displacement_plot', png_format),
'in2': ('motion_par', text_format),
'in3': ('correction_factors', text_format),
'in4': ('severe_motion_detection_report', text_format),
'in5': ('timestamps', directory_format)
})
pipeline.add(
'copy2dir',
CopyToDir(),
inputs={'in_files': (merge_inputs, 'out')},
outputs={'motion_detection_output': ('out_dir', directory_format)})
return pipeline
prepare_pet_pipeline = MultiStudy.translate(
'pet_mc', 'pet_data_preparation_pipeline')
pet_header_extraction_pipeline = MultiStudy.translate(
'pet_mc', 'pet_time_info_extraction_pipeline')
def motion_correction_pipeline(self, **name_maps):
if 'struct2align' in self.input_names:
StructAlignment = True
else:
StructAlignment = False
pipeline = self.new_pipeline(
name='pet_mc',
desc=("Given a folder with reconstructed PET data, this "
"pipeline will generate a motion corrected PET"
"image using information extracted from the MR-based "
"motion detection pipeline"),
citations=[fsl_cite],
name_maps=name_maps)
check_pet = pipeline.add(
'check_pet_data',
CheckPetMCInputs(),
inputs={
'pet_data': ('pet_data_prepared', directory_format),
'reference': ('ref_brain', nifti_gz_format)
},
requirements=[fsl_req.v('5.0.9'),
mrtrix_req.v('3.0rc3')])
if self.branch('dynamic_pet_mc'):
pipeline.connect_input('fixed_binning_mats', check_pet,
'motion_mats')
else:
pipeline.connect_input('average_mats', check_pet, 'motion_mats')
pipeline.connect_input('correction_factors', check_pet,
'corr_factors')
if StructAlignment:
struct_reg = pipeline.add('ref2structural_reg',
FLIRT(dof=6,
cost_func='normmi',
cost='normmi',
output_type='NIFTI_GZ'),
inputs={
'reference':
('ref_brain', nifti_gz_format),
'in_file':
('struct2align', nifti_gz_format)
},
requirements=[fsl_req.v('5.0.9')])
if self.branch('dynamic_pet_mc'):
pet_mc = pipeline.add('pet_mc',
PetImageMotionCorrection(),
inputs={
'pet_image': (check_pet, 'pet_images'),
'motion_mat': (check_pet, 'motion_mats'),
'pet2ref_mat': (check_pet, 'pet2ref_mat')
},
requirements=[fsl_req.v('5.0.9')],
iterfield=['pet_image', 'motion_mat'])
else:
pet_mc = pipeline.add(
'pet_mc',
PetImageMotionCorrection(),
inputs={'corr_factor': (check_pet, 'corr_factors')},
requirements=[fsl_req.v('5.0.9')],
iterfield=['corr_factor', 'pet_image', 'motion_mat'])
if StructAlignment:
pipeline.connect(struct_reg, 'out_matrix_file', pet_mc,
'structural2ref_regmat')
pipeline.connect_input('struct2align', pet_mc, 'structural_image')
if self.parameter('PET2MNI_reg'):
mni_reg = True
else:
mni_reg = False
if self.branch('dynamic_pet_mc'):
merge_mc = pipeline.add(
'merge_pet_mc',
fsl.Merge(dimension='t'),
inputs={'in_files': (pet_mc, 'pet_mc_image')},
requirements=[fsl_req.v('5.0.9')])
merge_no_mc = pipeline.add(
'merge_pet_no_mc',
fsl.Merge(dimension='t'),
inputs={'in_files': (pet_mc, 'pet_no_mc_image')},
requirements=[fsl_req.v('5.0.9')])
else:
static_mc = pipeline.add('static_mc_generation',
StaticPETImageGeneration(),
inputs={
'pet_mc_images':
(pet_mc, 'pet_mc_image'),
'pet_no_mc_images':
(pet_mc, 'pet_no_mc_image')
},
requirements=[fsl_req.v('5.0.9')])
merge_outputs = pipeline.add(
'merge_outputs',
Merge(3),
inputs={'in1': ('mean_displacement_plot', png_format)})
if not StructAlignment:
cropping = pipeline.add(
'pet_cropping',
PETFovCropping(x_min=self.parameter('crop_xmin'),
x_size=self.parameter('crop_xsize'),
y_min=self.parameter('crop_ymin'),
y_size=self.parameter('crop_ysize'),
z_min=self.parameter('crop_zmin'),
z_size=self.parameter('crop_zsize')))
if self.branch('dynamic_pet_mc'):
pipeline.connect(merge_mc, 'merged_file', cropping,
'pet_image')
else:
pipeline.connect(static_mc, 'static_mc', cropping, 'pet_image')
cropping_no_mc = pipeline.add(
'pet_no_mc_cropping',
PETFovCropping(x_min=self.parameter('crop_xmin'),
x_size=self.parameter('crop_xsize'),
y_min=self.parameter('crop_ymin'),
y_size=self.parameter('crop_ysize'),
z_min=self.parameter('crop_zmin'),
z_size=self.parameter('crop_zsize')))
if self.branch('dynamic_pet_mc'):
pipeline.connect(merge_no_mc, 'merged_file', cropping_no_mc,
'pet_image')
else:
pipeline.connect(static_mc, 'static_no_mc', cropping_no_mc,
'pet_image')
if mni_reg:
if self.branch('dynamic_pet_mc'):
t_mean = pipeline.add(
'PET_temporal_mean',
ImageMaths(op_string='-Tmean'),
inputs={'in_file': (cropping, 'pet_cropped')},
requirements=[fsl_req.v('5.0.9')])
reg_tmean2MNI = pipeline.add(
'reg2MNI',
AntsRegSyn(num_dimensions=3,
transformation='s',
out_prefix='reg2MNI',
num_threads=4,
ref_file=self.parameter('PET_template_MNI')),
wall_time=25,
requirements=[ants_req.v('2')])
if self.branch('dynamic_pet_mc'):
pipeline.connect(t_mean, 'out_file', reg_tmean2MNI,
'input_file')
merge_trans = pipeline.add('merge_transforms',
Merge(2),
inputs={
'in1': (reg_tmean2MNI,
'warp_file'),
'in2':
(reg_tmean2MNI, 'regmat')
},
wall_time=1)
apply_trans = pipeline.add(
'apply_trans',
ApplyTransforms(
reference_image=self.parameter('PET_template_MNI'),
interpolation='Linear',
input_image_type=3),
inputs={
'input_image': (cropping, 'pet_cropped'),
'transforms': (merge_trans, 'out')
},
wall_time=7,
mem_gb=24,
requirements=[ants_req.v('2')])
pipeline.connect(apply_trans, 'output_image',
merge_outputs, 'in2'),
else:
pipeline.connect(cropping, 'pet_cropped', reg_tmean2MNI,
'input_file')
pipeline.connect(reg_tmean2MNI, 'reg_file', merge_outputs,
'in2')
else:
pipeline.connect(cropping, 'pet_cropped', merge_outputs, 'in2')
pipeline.connect(cropping_no_mc, 'pet_cropped', merge_outputs,
'in3')
else:
if self.branch('dynamic_pet_mc'):
pipeline.connect(merge_mc, 'merged_file', merge_outputs, 'in2')
pipeline.connect(merge_no_mc, 'merged_file', merge_outputs,
'in3')
else:
pipeline.connect(static_mc, 'static_mc', merge_outputs, 'in2')
pipeline.connect(static_mc, 'static_no_mc', merge_outputs,
'in3')
# mcflirt = pipeline.add('mcflirt', MCFLIRT())
# 'in_file': (merge_mc_ps, 'merged_file'),
# cost='normmi',
copy2dir = pipeline.add('copy2dir',
CopyToDir(),
inputs={'in_files': (merge_outputs, 'out')})
if self.branch('dynamic_pet_mc'):
pipeline.connect_output('dynamic_motion_correction_results',
copy2dir, 'out_dir')
else:
pipeline.connect_output('static_motion_correction_results',
copy2dir, 'out_dir')
return pipeline
def create_motion_detection_class(name,
ref=None,
ref_type=None,
t1s=None,
t2s=None,
dwis=None,
epis=None,
pet_data_dir=None):
inputs = []
dct = {}
data_specs = []
run_pipeline = False
param_specs = [ParamSpec('ref_resampled_resolution', [1])]
if pet_data_dir is not None:
inputs.append(
InputFilesets('pet_data_dir', 'pet_data_dir', directory_format))
if not ref:
raise Exception('A reference image must be provided!')
if ref_type == 't1':
ref_study = T1Study
elif ref_type == 't2':
ref_study = T2Study
else:
raise Exception('{} is not a recognized ref_type!The available '
'ref_types are t1 or t2.'.format(ref_type))
study_specs = [SubStudySpec('ref', ref_study)]
ref_spec = {'coreg_ref_brain': 'ref_brain'}
inputs.append(InputFilesets('ref_magnitude', ref, dicom_format))
if t1s:
study_specs.extend([
SubStudySpec('t1_{}'.format(i), T1Study, ref_spec)
for i in range(len(t1s))
])
inputs.extend(
InputFilesets('t1_{}_magnitude'.format(i), t1_scan, dicom_format)
for i, t1_scan in enumerate(t1s))
run_pipeline = True
if t2s:
study_specs.extend([
SubStudySpec('t2_{}'.format(i), T2Study, ref_spec)
for i in range(len(t2s))
])
inputs.extend(
InputFilesets('t2_{}_magnitude'.format(i), t2_scan, dicom_format)
for i, t2_scan in enumerate(t2s))
run_pipeline = True
if epis:
epi_refspec = ref_spec.copy()
epi_refspec.update({
'coreg_ref_wmseg': 'ref_wm_seg',
'coreg_ref': 'ref_mag_preproc'
})
study_specs.extend(
SubStudySpec('epi_{}'.format(i), EpiSeriesStudy, epi_refspec)
for i in range(len(epis)))
inputs.extend(
InputFilesets('epi_{}_series'.format(i), epi_scan, dicom_format)
for i, epi_scan in enumerate(epis))
run_pipeline = True
if dwis:
unused_dwi = []
dwis_main = [x for x in dwis if x[-1] == '0']
dwis_ref = [x for x in dwis if x[-1] == '1']
dwis_opposite = [x for x in dwis if x[-1] == '-1']
b0_refspec = ref_spec.copy()
b0_refspec.update({
'coreg_ref_wmseg': 'ref_wm_seg',
'coreg_ref': 'ref_mag_preproc'
})
if dwis_main and not dwis_opposite:
logger.warning(
'No opposite phase encoding direction b0 provided. DWI '
'motion correction will be performed without distortion '
'correction. THIS IS SUB-OPTIMAL!')
study_specs.extend(
SubStudySpec('dwi_{}'.format(i), DwiStudy, ref_spec)
for i in range(len(dwis_main)))
inputs.extend(
InputFilesets('dwi_{}_series'.format(i), dwis_main_scan[0],
dicom_format)
for i, dwis_main_scan in enumerate(dwis_main))
if dwis_main and dwis_opposite:
study_specs.extend(
SubStudySpec('dwi_{}'.format(i), DwiStudy, ref_spec)
for i in range(len(dwis_main)))
inputs.extend(
InputFilesets('dwi_{}_series'.format(i), dwis_main[i][0],
dicom_format) for i in range(len(dwis_main)))
if len(dwis_main) <= len(dwis_opposite):
inputs.extend(
InputFilesets('dwi_{}_magnitude'.format(i),
dwis_opposite[i][0], dicom_format)
for i in range(len(dwis_main)))
else:
inputs.extend(
InputFilesets('dwi_{}_magnitude'.format(i),
dwis_opposite[0][0], dicom_format)
for i in range(len(dwis_main)))
if dwis_opposite and dwis_main and not dwis_ref:
study_specs.extend(
SubStudySpec('b0_{}'.format(i), DwiRefStudy, b0_refspec)
for i in range(len(dwis_opposite)))
inputs.extend(
InputFilesets('b0_{}_magnitude'.format(i), dwis_opposite[i][0],
dicom_format) for i in range(len(dwis_opposite)))
if len(dwis_opposite) <= len(dwis_main):
inputs.extend(
InputFilesets('b0_{}_reverse_phase'.format(i), dwis_main[i]
[0], dicom_format)
for i in range(len(dwis_opposite)))
else:
inputs.extend(
InputFilesets('b0_{}_reverse_phase'.format(i), dwis_main[0]
[0], dicom_format)
for i in range(len(dwis_opposite)))
elif dwis_opposite and dwis_ref:
min_index = min(len(dwis_opposite), len(dwis_ref))
study_specs.extend(
SubStudySpec('b0_{}'.format(i), DwiRefStudy, b0_refspec)
for i in range(min_index * 2))
inputs.extend(
InputFilesets('b0_{}_magnitude'.format(i), scan[0],
dicom_format)
for i, scan in enumerate(dwis_opposite[:min_index] +
dwis_ref[:min_index]))
inputs.extend(
InputFilesets('b0_{}_reverse_phase'.format(i), scan[0],
dicom_format)
for i, scan in enumerate(dwis_ref[:min_index] +
dwis_opposite[:min_index]))
unused_dwi = [
scan
for scan in dwis_ref[min_index:] + dwis_opposite[min_index:]
]
elif dwis_opposite or dwis_ref:
unused_dwi = [scan for scan in dwis_ref + dwis_opposite]
if unused_dwi:
logger.info(
'The following scans:\n{}\nwere not assigned during the DWI '
'motion detection initialization (probably a different number '
'of main DWI scans and b0 images was provided). They will be '
'processed os "other" scans.'.format('\n'.join(
s[0] for s in unused_dwi)))
study_specs.extend(
SubStudySpec('t2_{}'.format(i), T2Study, ref_spec)
for i in range(len(t2s),
len(t2s) + len(unused_dwi)))
inputs.extend(
InputFilesets('t2_{}_magnitude'.format(i), scan[0],
dicom_format)
for i, scan in enumerate(unused_dwi, start=len(t2s)))
run_pipeline = True
if not run_pipeline:
raise Exception('At least one scan, other than the reference, must be '
'provided!')
dct['add_substudy_specs'] = study_specs
dct['add_data_specs'] = data_specs
dct['__metaclass__'] = MultiStudyMetaClass
dct['add_param_specs'] = param_specs
return MultiStudyMetaClass(name, (MotionDetectionMixin, ), dct), inputs
class BoldStudy(EpiSeriesStudy, metaclass=StudyMetaClass):
desc = "Functional MRI BOLD MRI contrast"
add_data_specs = [
InputFilesetSpec('train_data',
rfile_format,
optional=True,
frequency='per_study'),
FilesetSpec('hand_label_noise', text_format,
'fix_preparation_pipeline'),
FilesetSpec('labelled_components', text_format,
'fix_classification_pipeline'),
FilesetSpec('cleaned_file', nifti_gz_format,
'fix_regression_pipeline'),
FilesetSpec('filtered_data', nifti_gz_format,
'rsfMRI_filtering_pipeline'),
FilesetSpec('mc_par', par_format, 'rsfMRI_filtering_pipeline'),
FilesetSpec('melodic_ica', zip_format,
'single_subject_melodic_pipeline'),
FilesetSpec('fix_dir', zip_format, 'fix_preparation_pipeline'),
FilesetSpec('normalized_ts', nifti_gz_format,
'timeseries_normalization_to_atlas_pipeline'),
FilesetSpec('smoothed_ts', nifti_gz_format, 'smoothing_pipeline')
]
add_param_specs = [
ParamSpec('component_threshold', 20),
ParamSpec('motion_reg', True),
ParamSpec('highpass', 0.01),
ParamSpec('brain_thresh_percent', 5),
ParamSpec('group_ica_components', 15)
]
primary_bids_selector = BidsInputs(spec_name='series',
type='bold',
valid_formats=(nifti_gz_x_format,
nifti_gz_format))
default_bids_inputs = [
primary_bids_selector,
BidsAssocInput(spec_name='field_map_phase',
primary=primary_bids_selector,
association='phasediff',
format=nifti_gz_format,
drop_if_missing=True),
BidsAssocInput(spec_name='field_map_mag',
primary=primary_bids_selector,
association='phasediff',
type='magnitude',
format=nifti_gz_format,
drop_if_missing=True)
]
def rsfMRI_filtering_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='rsfMRI_filtering',
desc=("Spatial and temporal rsfMRI filtering"),
citations=[fsl_cite],
name_maps=name_maps)
afni_mc = pipeline.add(
'AFNI_MC',
Volreg(zpad=1,
out_file='rsfmri_mc.nii.gz',
oned_file='prefiltered_func_data_mcf.par'),
inputs={'in_file': ('series_preproc', nifti_gz_format)},
outputs={'mc_par': ('oned_file', par_format)},
wall_time=5,
requirements=[afni_req.v('16.2.10')])
filt = pipeline.add('Tproject',
Tproject(stopband=(0, 0.01),
polort=3,
blur=3,
out_file='filtered_func_data.nii.gz'),
inputs={
'delta_t': ('tr', float),
'mask':
(self.brain_mask_spec_name, nifti_gz_format),
'in_file': (afni_mc, 'out_file')
},
wall_time=5,
requirements=[afni_req.v('16.2.10')])
meanfunc = pipeline.add('meanfunc',
ImageMaths(op_string='-Tmean',
suffix='_mean',
output_type='NIFTI_GZ'),
wall_time=5,
inputs={'in_file': (afni_mc, 'out_file')},
requirements=[fsl_req.v('5.0.10')])
pipeline.add('add_mean',
ImageMaths(op_string='-add', output_type='NIFTI_GZ'),
inputs={
'in_file': (filt, 'out_file'),
'in_file2': (meanfunc, 'out_file')
},
outputs={'filtered_data': ('out_file', nifti_gz_format)},
wall_time=5,
requirements=[fsl_req.v('5.0.10')])
return pipeline
def single_subject_melodic_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='MelodicL1',
desc=("Single subject ICA analysis using FSL MELODIC."),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add('melodic_L1',
MELODIC(
no_bet=True,
bg_threshold=self.parameter('brain_thresh_percent'),
report=True,
out_stats=True,
mm_thresh=0.5,
out_dir='melodic_ica',
output_type='NIFTI_GZ'),
inputs={
'mask': (self.brain_mask_spec_name, nifti_gz_format),
'tr_sec': ('tr', float),
'in_files': ('filtered_data', nifti_gz_format)
},
outputs={'melodic_ica': ('out_dir', directory_format)},
wall_time=15,
requirements=[fsl_req.v('5.0.10')])
return pipeline
def fix_preparation_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='prepare_fix',
desc=("Pipeline to create the right folder structure before "
"running FIX"),
citations=[fsl_cite],
name_maps=name_maps)
if self.branch('coreg_to_tmpl_method', 'ants'):
struct_ants2fsl = pipeline.add(
'struct_ants2fsl',
ANTs2FSLMatrixConversion(ras2fsl=True),
inputs={
'reference_file': ('template_brain', nifti_gz_format),
'itk_file': ('coreg_to_tmpl_ants_mat', text_matrix_format),
'source_file': ('coreg_ref_brain', nifti_gz_format)
},
requirements=[c3d_req.v('1.0.0')])
struct_matrix = (struct_ants2fsl, 'fsl_matrix')
else:
struct_matrix = ('coreg_to_tmpl_fsl_mat', text_matrix_format)
# if self.branch('coreg_method', 'ants'):
# epi_ants2fsl = pipeline.add(
# 'epi_ants2fsl',
# ANTs2FSLMatrixConversion(
# ras2fsl=True),
# inputs={
# 'source_file': ('brain', nifti_gz_format),
# 'itk_file': ('coreg_ants_mat', text_matrix_format),
# 'reference_file': ('coreg_ref_brain', nifti_gz_format)},
# requirements=[c3d_req.v('1.0.0')])
MNI2t1 = pipeline.add('MNI2t1',
ConvertXFM(invert_xfm=True),
inputs={'in_file': struct_matrix},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
struct2epi = pipeline.add(
'struct2epi',
ConvertXFM(invert_xfm=True),
inputs={'in_file': ('coreg_fsl_mat', text_matrix_format)},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
meanfunc = pipeline.add(
'meanfunc',
ImageMaths(op_string='-Tmean',
suffix='_mean',
output_type='NIFTI_GZ'),
inputs={'in_file': ('series_preproc', nifti_gz_format)},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
pipeline.add('prep_fix',
PrepareFIX(),
inputs={
'melodic_dir': ('melodic_ica', directory_format),
't1_brain': ('coreg_ref_brain', nifti_gz_format),
'mc_par': ('mc_par', par_format),
'epi_brain_mask': ('brain_mask', nifti_gz_format),
'epi_preproc': ('series_preproc', nifti_gz_format),
'filtered_epi': ('filtered_data', nifti_gz_format),
'epi2t1_mat': ('coreg_fsl_mat', text_matrix_format),
't12MNI_mat': (struct_ants2fsl, 'fsl_matrix'),
'MNI2t1_mat': (MNI2t1, 'out_file'),
't12epi_mat': (struct2epi, 'out_file'),
'epi_mean': (meanfunc, 'out_file')
},
outputs={
'fix_dir': ('fix_dir', directory_format),
'hand_label_noise': ('hand_label_file', text_format)
})
return pipeline
def fix_classification_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='fix_classification',
desc=("Automatic classification of noisy components from the "
"rsfMRI data using fsl FIX."),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
"fix",
FSLFIX(component_threshold=self.parameter('component_threshold'),
motion_reg=self.parameter('motion_reg'),
classification=True),
inputs={
"feat_dir": ("fix_dir", directory_format),
"train_data": ("train_data", rfile_format)
},
outputs={'labelled_components': ('label_file', text_format)},
wall_time=30,
requirements=[fsl_req.v('5.0.9'),
fix_req.v('1.0')])
return pipeline
def fix_regression_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='signal_regression',
desc=("Regression of the noisy components from the rsfMRI data "
"using a python implementation equivalent to that in FIX."),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
"signal_reg",
SignalRegression(motion_regression=self.parameter('motion_reg'),
highpass=self.parameter('highpass')),
inputs={
"fix_dir": ("fix_dir", directory_format),
"labelled_components": ("labelled_components", text_format)
},
outputs={'cleaned_file': ('output', nifti_gz_format)},
wall_time=30,
requirements=[fsl_req.v('5.0.9'),
fix_req.v('1.0')])
return pipeline
def timeseries_normalization_to_atlas_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='timeseries_normalization_to_atlas_pipeline',
desc=("Apply ANTs transformation to the fmri filtered file to "
"normalize it to MNI 2mm."),
citations=[fsl_cite],
name_maps=name_maps)
merge_trans = pipeline.add('merge_transforms',
NiPypeMerge(3),
inputs={
'in1': ('coreg_to_tmpl_ants_warp',
nifti_gz_format),
'in2': ('coreg_to_tmpl_ants_mat',
text_matrix_format),
'in3':
('coreg_matrix', text_matrix_format)
},
wall_time=1)
pipeline.add(
'ApplyTransform',
ApplyTransforms(interpolation='Linear', input_image_type=3),
inputs={
'reference_image': ('template_brain', nifti_gz_format),
'input_image': ('cleaned_file', nifti_gz_format),
'transforms': (merge_trans, 'out')
},
outputs={'normalized_ts': ('output_image', nifti_gz_format)},
wall_time=7,
mem_gb=24,
requirements=[ants_req.v('2')])
return pipeline
def smoothing_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='smoothing_pipeline',
desc=("Spatial smoothing of the normalized fmri file"),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add('3dBlurToFWHM',
BlurToFWHM(fwhm=5, out_file='smoothed_ts.nii.gz'),
inputs={
'mask': ('template_mask', nifti_gz_format),
'in_file': ('normalized_ts', nifti_gz_format)
},
outputs={'smoothed_ts': ('out_file', nifti_gz_format)},
wall_time=5,
requirements=[afni_req.v('16.2.10')])
return pipeline
def create_multi_fmri_class(name,
t1,
epis,
epi_number,
echo_spacing,
fm_mag=None,
fm_phase=None,
run_regression=False):
inputs = []
dct = {}
data_specs = []
param_specs = []
output_files = []
distortion_correction = False
if fm_mag and fm_phase:
logger.info('Both magnitude and phase field map images provided. EPI '
'ditortion correction will be performed.')
distortion_correction = True
elif fm_mag or fm_phase:
logger.info(
'In order to perform EPI ditortion correction both magnitude '
'and phase field map images must be provided.')
else:
logger.info(
'No field map image provided. Distortion correction will not be'
'performed.')
study_specs = [SubStudySpec('t1', T1Study)]
ref_spec = {'t1_brain': 'coreg_ref_brain'}
inputs.append(
InputFilesets('t1_primary', t1, dicom_format, is_regex=True, order=0))
epi_refspec = ref_spec.copy()
epi_refspec.update({
't1_wm_seg': 'coreg_ref_wmseg',
't1_preproc': 'coreg_ref',
'train_data': 'train_data'
})
study_specs.append(SubStudySpec('epi_0', BoldStudy, epi_refspec))
if epi_number > 1:
epi_refspec.update({
't1_wm_seg':
'coreg_ref_wmseg',
't1_preproc':
'coreg_ref',
'train_data':
'train_data',
'epi_0_coreg_to_tmpl_warp':
'coreg_to_tmpl_warp',
'epi_0_coreg_to_tmpl_ants_mat':
'coreg_to_tmpl_ants_mat'
})
study_specs.extend(
SubStudySpec('epi_{}'.format(i), BoldStudy, epi_refspec)
for i in range(1, epi_number))
study_specs.extend(
SubStudySpec('epi_{}'.format(i), BoldStudy, epi_refspec)
for i in range(epi_number))
for i in range(epi_number):
inputs.append(
InputFilesets('epi_{}_primary'.format(i),
epis,
dicom_format,
order=i,
is_regex=True))
# inputs.extend(InputFilesets(
# 'epi_{}_hand_label_noise'.format(i), text_format,
# 'hand_label_noise_{}'.format(i+1))
# for i in range(epi_number))
param_specs.append(
ParamSpec('epi_{}_fugue_echo_spacing'.format(i), echo_spacing))
if distortion_correction:
inputs.extend(
InputFilesets('epi_{}_field_map_mag'.format(i),
fm_mag,
dicom_format,
dicom_tags={IMAGE_TYPE_TAG: MAG_IMAGE_TYPE},
is_regex=True,
order=0) for i in range(epi_number))
inputs.extend(
InputFilesets('epi_{}_field_map_phase'.format(i),
fm_phase,
dicom_format,
dicom_tags={IMAGE_TYPE_TAG: PHASE_IMAGE_TYPE},
is_regex=True,
order=0) for i in range(epi_number))
if run_regression:
output_files.extend('epi_{}_smoothed_ts'.format(i)
for i in range(epi_number))
else:
output_files.extend('epi_{}_fix_dir'.format(i)
for i in range(epi_number))
dct['add_substudy_specs'] = study_specs
dct['add_data_specs'] = data_specs
dct['add_param_specs'] = param_specs
dct['__metaclass__'] = MultiStudyMetaClass
return (MultiStudyMetaClass(name, (MultiBoldMixin, ),
dct), inputs, output_files)
class DynamicPetStudy(PetStudy, metaclass=StudyMetaClass):
add_data_specs = [
InputFilesetSpec('pet_volumes', nifti_gz_format),
InputFilesetSpec('regression_map', nifti_gz_format),
FilesetSpec('pet_image', nifti_gz_format, 'Extract_vol_pipeline'),
FilesetSpec('registered_volumes', nifti_gz_format,
'ApplyTransform_pipeline'),
FilesetSpec('detrended_volumes', nifti_gz_format,
'Baseline_Removal_pipeline'),
FilesetSpec('spatial_map', nifti_gz_format,
'Dual_Regression_pipeline'),
FilesetSpec('ts', png_format, 'Dual_Regression_pipeline')
]
add_param_specs = [
ParamSpec('trans_template',
os.path.join(template_path, 'PET_template.nii.gz')),
ParamSpec('base_remove_th', 0),
ParamSpec('base_remove_binarize', False),
ParamSpec('regress_th', 0),
ParamSpec('regress_binarize', False)
]
primary_scan_name = 'pet_volumes'
def Extract_vol_pipeline(self, **kwargs):
pipeline = self.new_pipeline(
name='Extract_volume',
desc=('Extract the last volume of the 4D PET timeseries'),
citations=[],
**kwargs)
pipeline.add('fslroi',
ExtractROI(roi_file='vol.nii.gz', t_min=79, t_size=1),
inputs={'in_file': ('pet_volumes', nifti_gz_format)},
outputs={'pet_image': ('roi_file', nifti_gz_format)})
return pipeline
def ApplyTransform_pipeline(self, **kwargs):
pipeline = self.new_pipeline(
name='applytransform',
desc=('Apply transformation the the 4D PET timeseries'),
citations=[],
**kwargs)
merge_trans = pipeline.add('merge_transforms',
Merge(2),
inputs={
'in1': ('warp_file', nifti_gz_format),
'in2':
('affine_mat', text_matrix_format)
})
pipeline.add(
'ApplyTransform',
ApplyTransforms(reference_image=self.parameter('trans_template'),
interpolation='Linear',
input_image_type=3),
inputs={
'input_image': ('pet_volumes', nifti_gz_format),
'transforms': (merge_trans, 'out')
},
outputs={'registered_volumes': ('output_image', nifti_gz_format)})
return pipeline
def Baseline_Removal_pipeline(self, **kwargs):
pipeline = self.new_pipeline(name='Baseline_removal',
desc=('PET dual regression'),
citations=[],
**kwargs)
pipeline.add(
'Baseline_removal',
GlobalTrendRemoval(),
inputs={'volume': ('registered_volumes', nifti_gz_format)},
outputs={'detrended_volumes': ('detrended_file', nifti_gz_format)})
return pipeline
def Dual_Regression_pipeline(self, **kwargs):
pipeline = self.new_pipeline(name='Dual_regression',
desc=('PET dual regression'),
citations=[],
**kwargs)
pipeline.add('PET_dr',
PETdr(threshold=self.parameter('regress_th'),
binarize=self.parameter('regress_binarize')),
inputs={
'volume': ('detrended_volumes', nifti_gz_format),
'regression_map': ('regression_map', nifti_gz_format)
},
outputs={
'spatial_map': ('spatial_map', nifti_gz_format),
'ts': ('timecourse', png_format)
})
return pipeline
class T1Study(T2Study, metaclass=StudyMetaClass):
desc = "T1-weighted MRI contrast"
add_data_specs = [
FilesetSpec('fs_recon_all', zip_format, 'freesurfer_pipeline'),
InputFilesetSpec(
't2_coreg',
STD_IMAGE_FORMATS,
optional=True,
desc=("A coregistered T2 image to use in freesurfer to help "
"distinguish the peel surface")),
# Templates
InputFilesetSpec('suit_mask',
STD_IMAGE_FORMATS,
frequency='per_study',
default=LocalReferenceData('SUIT', nifti_format)),
FilesetSpec('five_tissue_type',
mrtrix_image_format,
'gen_5tt_pipeline',
desc=("A segmentation image taken from freesurfer output "
"and simplified into 5 tissue types. Used in ACT "
"streamlines tractography"))
] + [
FilesetSpec('aparc_stats_{}_{}_table'.format(h, m),
text_format,
'aparc_stats_table_pipeline',
frequency='per_visit',
pipeline_args={
'hemisphere': h,
'measure': m
},
desc=("Table of {} of {} per parcellated segment".format(
m, h.upper())))
for h, m in itertools.product(
('lh', 'rh'), ('volume', 'thickness', 'thicknessstd', 'meancurv',
'gauscurv', 'foldind', 'curvind'))
]
add_param_specs = [
# MriStudy.param_spec('bet_method').with_new_choices(default='opti_bet'),
SwitchSpec('bet_robust', False),
SwitchSpec('bet_reduce_bias', True),
SwitchSpec('aparc_atlas',
'desikan-killiany',
choices=('desikan-killiany', 'destrieux', 'DKT')),
ParamSpec('bet_f_threshold', 0.1),
ParamSpec('bet_g_threshold', 0.0)
]
default_bids_inputs = [
BidsInputs(spec_name='magnitude',
type='T1w',
valid_formats=(nifti_gz_x_format, nifti_gz_format))
]
primary_scan_name = 'magnitude'
def freesurfer_pipeline(self, **name_maps):
"""
Segments grey matter, white matter and CSF from T1 images using
SPM "NewSegment" function.
NB: Default values come from the W2MHS toolbox
"""
pipeline = self.new_pipeline(name='segmentation',
name_maps=name_maps,
desc="Segment white/grey matter and csf",
citations=copy(freesurfer_cites))
# FS ReconAll node
recon_all = pipeline.add(
'recon_all',
interface=ReconAll(directive='all',
openmp=self.processor.num_processes),
inputs={'T1_files': (self.preproc_spec_name, nifti_gz_format)},
requirements=[freesurfer_req.v('5.3')],
wall_time=2000)
if self.provided('t2_coreg'):
pipeline.connect_input('t2_coreg', recon_all, 'T2_file',
nifti_gz_format)
recon_all.inputs.use_T2 = True
# Wrapper around os.path.join
pipeline.add('join',
JoinPath(),
inputs={
'dirname': (recon_all, 'subjects_dir'),
'filename': (recon_all, 'subject_id')
},
outputs={'fs_recon_all': ('path', directory_format)})
return pipeline
def segmentation_pipeline(self, **name_maps):
pipeline = super(T1Study, self).segmentation_pipeline(img_type=1,
**name_maps)
return pipeline
def gen_5tt_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='gen5tt',
name_maps=name_maps,
desc=("Generate 5-tissue-type image used for Anatomically-"
"Constrained Tractography (ACT)"))
aseg_path = pipeline.add(
'aseg_path',
AppendPath(sub_paths=['mri', 'aseg.mgz']),
inputs={'base_path': ('fs_recon_all', directory_format)})
pipeline.add(
'gen5tt',
mrtrix3.Generate5tt(algorithm='freesurfer', out_file='5tt.mif'),
inputs={'in_file': (aseg_path, 'out_path')},
outputs={'five_tissue_type': ('out_file', mrtrix_image_format)},
requirements=[mrtrix_req.v('3.0rc3'),
freesurfer_req.v('6.0')])
return pipeline
def aparc_stats_table_pipeline(self, measure, hemisphere, **name_maps):
pipeline = self.new_pipeline(
name='aparc_stats_{}_{}'.format(hemisphere, measure),
name_maps=name_maps,
desc=("Extract statistics from freesurfer outputs"))
copy_to_dir = pipeline.add('copy_to_subjects_dir',
CopyToDir(),
inputs={
'in_files':
('fs_recon_all', directory_format),
'file_names': (self.SUBJECT_ID, int)
},
joinsource=self.SUBJECT_ID,
joinfield=['in_files', 'file_names'])
if self.branch('aparc_atlas', 'desikan-killiany'):
parc = 'aparc'
elif self.branch('aparc_atlas', 'destrieux'):
parc = 'aparc.a2009s'
elif self.branch('aparc_atlas', 'DKT'):
parc = 'aparc.DKTatlas40'
else:
self.unhandled_branch('aparc_atlas')
pipeline.add('aparc_stats',
AparcStats(measure=measure,
hemisphere=hemisphere,
parc=parc),
inputs={
'subjects_dir': (copy_to_dir, 'out_dir'),
'subjects': (copy_to_dir, 'file_names')
},
outputs={
'aparc_stats_{}_{}_table'.format(hemisphere, measure):
('tablefile', text_format)
},
requirements=[freesurfer_req.v('5.3')])
return pipeline
class PetStudy(Study, metaclass=StudyMetaClass):
add_param_specs = [
ParamSpec('ica_n_components', 2),
ParamSpec('ica_type', 'spatial'),
ParamSpec('norm_transformation', 's'),
ParamSpec('norm_dim', 3),
ParamSpec('norm_template',
os.path.join(template_path, 'PET_template.nii.gz')),
ParamSpec('crop_xmin', 100),
ParamSpec('crop_xsize', 130),
ParamSpec('crop_ymin', 100),
ParamSpec('crop_ysize', 130),
ParamSpec('crop_zmin', 20),
ParamSpec('crop_zsize', 100),
ParamSpec('image_orientation_check', False)
]
add_data_specs = [
InputFilesetSpec('list_mode', list_mode_format),
InputFilesetSpec('registered_volumes', nifti_gz_format),
InputFilesetSpec('pet_image', nifti_gz_format),
InputFilesetSpec('pet_data_dir', directory_format),
InputFilesetSpec('pet_recon_dir', directory_format),
FilesetSpec('pet_recon_dir_prepared', directory_format,
'pet_data_preparation_pipeline'),
FilesetSpec('decomposed_file', nifti_gz_format, 'ICA_pipeline'),
FilesetSpec('timeseries', nifti_gz_format, 'ICA_pipeline'),
FilesetSpec('mixing_mat', text_format, 'ICA_pipeline'),
FilesetSpec('registered_volume', nifti_gz_format,
'Image_normalization_pipeline'),
FilesetSpec('warp_file', nifti_gz_format,
'Image_normalization_pipeline'),
FilesetSpec('invwarp_file', nifti_gz_format,
'Image_normalization_pipeline'),
FilesetSpec('affine_mat', text_matrix_format,
'Image_normalization_pipeline'),
FieldSpec('pet_duration', int, 'pet_time_info_extraction_pipeline'),
FieldSpec('pet_end_time', str, 'pet_time_info_extraction_pipeline'),
FieldSpec('pet_start_time', str, 'pet_time_info_extraction_pipeline'),
InputFieldSpec('time_offset', int),
InputFieldSpec('temporal_length', float),
InputFieldSpec('num_frames', int),
FilesetSpec('ssrb_sinograms', directory_format,
'sinogram_unlisting_pipeline')
]
def ICA_pipeline(self, **kwargs):
pipeline = self.new_pipeline(
name='ICA',
desc=('Decompose a 4D fileset into a set of independent '
'components using FastICA'),
citations=[],
**kwargs)
pipeline.add(
'ICA',
FastICA(n_components=self.parameter('ica_n_components'),
ica_type=self.parameter('ica_type')),
inputs={'volume': ('registered_volumes', nifti_gz_format)},
ouputs={
'decomposed_file': ('ica_decomposition', nifti_gz_format),
'timeseries': ('ica_timeseries', nifti_gz_format),
'mixing_mat': ('mixing_mat', text_format)
})
return pipeline
def Image_normalization_pipeline(self, **kwargs):
pipeline = self.new_pipeline(
name='Image_registration',
desc=('Image registration to a template using ANTs'),
citations=[],
**kwargs)
pipeline.add('ANTs',
AntsRegSyn(
out_prefix='vol2template',
num_dimensions=self.parameter('norm_dim'),
num_threads=self.processor.num_processes,
transformation=self.parameter('norm_transformation'),
ref_file=self.parameter('norm_template')),
inputs={'input_file': ('pet_image', nifti_gz_format)},
ouputs={
'registered_volume': ('reg_file', nifti_gz_format),
'warp_file': ('warp_file', nifti_gz_format),
'invwarp_file': ('inv_warp', nifti_gz_format),
'affine_mat': ('regmat', text_matrix_format)
})
return pipeline
def pet_data_preparation_pipeline(self, **kwargs):
pipeline = self.new_pipeline(
name='pet_data_preparation',
desc=("Given a folder with reconstructed PET data, this "
"pipeline will prepare the data for the motion "
"correction"),
citations=[],
**kwargs)
pipeline.add('prepare_pet',
PreparePetDir(image_orientation_check=self.parameter(
'image_orientation_check')),
inputs={'pet_dir': ('pet_recon_dir', directory_format)},
ouputs={
'pet_recon_dir_prepared':
('pet_dir_prepared', directory_format)
},
requirements=[mrtrix_req.v('3.0rc3'),
fsl_req.v('5.0.9')])
return pipeline
def pet_time_info_extraction_pipeline(self, **kwargs):
pipeline = self.new_pipeline(
name='pet_info_extraction',
desc=("Extract PET time info from list-mode header."),
citations=[],
**kwargs)
pipeline.add(
'PET_time_info',
PetTimeInfo(),
inputs={'pet_data_dir': ('pet_data_dir', directory_format)},
ouputs={
'pet_end_time': ('pet_end_time', float),
'pet_start_time': ('pet_start_time', str),
'pet_duration': ('pet_duration', int)
})
return pipeline
def sinogram_unlisting_pipeline(self, **kwargs):
pipeline = self.new_pipeline(
name='prepare_sinogram',
desc=('Unlist pet listmode data into several sinograms and '
'perform ssrb compression to prepare data for motion '
'detection using PCA pipeline.'),
citations=[],
**kwargs)
if not self.provided('list_mode'):
raise BananaUsageError(
"'list_mode' was not provided as an input to the study "
"so cannot perform sinogram unlisting")
prepare_inputs = pipeline.add('prepare_inputs',
PrepareUnlistingInputs(),
inputs={
'list_mode':
('list_mode', list_mode_format),
'time_offset': ('time_offset', int),
'num_frames': ('num_frames', int),
'temporal_len':
('temporal_length', float)
})
unlisting = pipeline.add(
'unlisting',
PETListModeUnlisting(),
inputs={'list_inputs': (prepare_inputs, 'out')},
iterfield=['list_inputs'])
ssrb = pipeline.add(
'ssrb',
SSRB(),
inputs={'unlisted_sinogram': (unlisting, 'pet_sinogram')},
requirements=[stir_req.v('3.0')])
pipeline.add(
'merge_sinograms',
MergeUnlistingOutputs(),
inputs={'sinograms': (ssrb, 'ssrb_sinograms')},
ouputs={'ssrb_sinograms': ('sinogram_folder', directory_format)},
joinsource='unlisting',
joinfield=['sinograms'])
return pipeline
class DwiStudy(EpiSeriesStudy, metaclass=StudyMetaClass):
desc = "Diffusion-weighted MRI contrast"
add_data_specs = [
InputFilesetSpec('anat_5tt', mrtrix_image_format,
desc=("A co-registered segmentation image taken from "
"freesurfer output and simplified into 5 tissue"
" types. Used in ACT streamlines tractography"),
optional=True),
InputFilesetSpec('anat_fs_recon_all', zip_format, optional=True,
desc=("Co-registered freesurfer recon-all output. "
"Used in building the connectome")),
InputFilesetSpec('reverse_phase', STD_IMAGE_FORMATS, optional=True),
FilesetSpec('grad_dirs', fsl_bvecs_format, 'preprocess_pipeline'),
FilesetSpec('grad_dirs_coreg', fsl_bvecs_format,
'series_coreg_pipeline',
desc=("The gradient directions coregistered to the "
"orientation of the coreg reference")),
FilesetSpec('bvalues', fsl_bvals_format, 'preprocess_pipeline',
desc=("")),
FilesetSpec('eddy_par', eddy_par_format, 'preprocess_pipeline',
desc=("")),
FilesetSpec('noise_residual', mrtrix_image_format,
'preprocess_pipeline',
desc=("")),
FilesetSpec('tensor', nifti_gz_format, 'tensor_pipeline',
desc=("")),
FilesetSpec('fa', nifti_gz_format, 'tensor_metrics_pipeline',
desc=("")),
FilesetSpec('adc', nifti_gz_format, 'tensor_metrics_pipeline',
desc=("")),
FilesetSpec('wm_response', text_format, 'response_pipeline',
desc=("")),
FilesetSpec('gm_response', text_format, 'response_pipeline',
desc=("")),
FilesetSpec('csf_response', text_format, 'response_pipeline',
desc=("")),
FilesetSpec('avg_response', text_format, 'average_response_pipeline',
desc=("")),
FilesetSpec('wm_odf', mrtrix_image_format, 'fod_pipeline',
desc=("")),
FilesetSpec('gm_odf', mrtrix_image_format, 'fod_pipeline',
desc=("")),
FilesetSpec('csf_odf', mrtrix_image_format, 'fod_pipeline',
desc=("")),
FilesetSpec('norm_intensity', mrtrix_image_format,
'intensity_normalisation_pipeline',
desc=("")),
FilesetSpec('norm_intens_fa_template', mrtrix_image_format,
'intensity_normalisation_pipeline', frequency='per_study',
desc=("")),
FilesetSpec('norm_intens_wm_mask', mrtrix_image_format,
'intensity_normalisation_pipeline', frequency='per_study',
desc=("")),
FilesetSpec('global_tracks', mrtrix_track_format,
'global_tracking_pipeline',
desc=("")),
FilesetSpec('wm_mask', mrtrix_image_format,
'global_tracking_pipeline',
desc=("")),
FilesetSpec('connectome', csv_format, 'connectome_pipeline',
desc=(""))]
add_param_specs = [
ParamSpec('multi_tissue', True,
desc=("")),
ParamSpec('preproc_pe_dir', None, dtype=str,
desc=("")),
ParamSpec('tbss_skel_thresh', 0.2,
desc=("")),
ParamSpec('fsl_mask_f', 0.25,
desc=("")),
ParamSpec('bet_robust', True,
desc=("")),
ParamSpec('bet_f_threshold', 0.2,
desc=("")),
ParamSpec('bet_reduce_bias', False,
desc=("")),
ParamSpec('num_global_tracks', int(1e9),
desc=("")),
ParamSpec('global_tracks_cutoff', 0.05,
desc=("")),
SwitchSpec('preproc_denoise', False,
desc=("")),
SwitchSpec('response_algorithm', 'tax',
('tax', 'dhollander', 'msmt_5tt'),
desc=("")),
SwitchSpec('fod_algorithm', 'csd', ('csd', 'msmt_csd'),
desc=("")),
MriStudy.param_spec('bet_method').with_new_choices('mrtrix'),
SwitchSpec('reorient2std', False,
desc=(""))]
primary_bids_input = BidsInputs(
spec_name='series', type='dwi',
valid_formats=(nifti_gz_x_format, nifti_gz_format))
default_bids_inputs = [primary_bids_input,
BidsAssocInputs(
spec_name='bvalues',
primary=primary_bids_input,
association='grads',
type='bval',
format=fsl_bvals_format),
BidsAssocInputs(
spec_name='grad_dirs',
primary=primary_bids_input,
association='grads',
type='bvec',
format=fsl_bvecs_format),
BidsAssocInputs(
spec_name='reverse_phase',
primary=primary_bids_input,
association='epi',
format=nifti_gz_format,
drop_if_missing=True)]
RECOMMENDED_NUM_SESSIONS_FOR_INTENS_NORM = 5
primary_scan_name = 'series'
@property
def multi_tissue(self):
return self.branch('response_algorithm',
('msmt_5tt', 'dhollander'))
def fsl_grads(self, pipeline, coregistered=True):
"Adds and returns a node to the pipeline to merge the FSL grads and "
"bvecs"
try:
fslgrad = pipeline.node('fslgrad')
except ArcanaNameError:
if self.is_coregistered and coregistered:
grad_dirs = 'grad_dirs_coreg'
else:
grad_dirs = 'grad_dirs'
# Gradient merge node
fslgrad = pipeline.add(
"fslgrad",
MergeTuple(2),
inputs={
'in1': (grad_dirs, fsl_bvecs_format),
'in2': ('bvalues', fsl_bvals_format)})
return (fslgrad, 'out')
def extract_magnitude_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
'extract_magnitude',
desc="Extracts the first b==0 volume from the series",
citations=[],
name_maps=name_maps)
dwiextract = pipeline.add(
'dwiextract',
ExtractDWIorB0(
bzero=True,
out_ext='.nii.gz'),
inputs={
'in_file': ('series', nifti_gz_format),
'fslgrad': self.fsl_grads(pipeline, coregistered=False)},
requirements=[mrtrix_req.v('3.0rc3')])
pipeline.add(
"extract_first_vol",
MRConvert(
coord=(3, 0)),
inputs={
'in_file': (dwiextract, 'out_file')},
outputs={
'magnitude': ('out_file', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
return pipeline
def preprocess_pipeline(self, **name_maps):
"""
Performs a series of FSL preprocessing steps, including Eddy and Topup
Parameters
----------
phase_dir : str{AP|LR|IS}
The phase encode direction
"""
# Determine whether we can correct for distortion, i.e. if reference
# scans are provided
# Include all references
references = [fsl_cite, eddy_cite, topup_cite,
distort_correct_cite, n4_cite]
if self.branch('preproc_denoise'):
references.extend(dwidenoise_cites)
pipeline = self.new_pipeline(
name='preprocess',
name_maps=name_maps,
desc=(
"Preprocess dMRI studies using distortion correction"),
citations=references)
# Create nodes to gradients to FSL format
if self.input('series').format == dicom_format:
extract_grad = pipeline.add(
"extract_grad",
ExtractFSLGradients(),
inputs={
'in_file': ('series', dicom_format)},
outputs={
'grad_dirs': ('bvecs_file', fsl_bvecs_format),
'bvalues': ('bvals_file', fsl_bvals_format)},
requirements=[mrtrix_req.v('3.0rc3')])
grad_fsl_inputs = {'in1': (extract_grad, 'bvecs_file'),
'in2': (extract_grad, 'bvals_file')}
elif self.provided('grad_dirs') and self.provided('bvalues'):
grad_fsl_inputs = {'in1': ('grad_dirs', fsl_bvecs_format),
'in2': ('bvalues', fsl_bvals_format)}
else:
raise BananaUsageError(
"Either input 'magnitude' image needs to be in DICOM format "
"or gradient directions and b-values need to be explicitly "
"provided to {}".format(self))
# Gradient merge node
grad_fsl = pipeline.add(
"grad_fsl",
MergeTuple(2),
inputs=grad_fsl_inputs)
gradients = (grad_fsl, 'out')
# Create node to reorient preproc out_file
if self.branch('reorient2std'):
reorient = pipeline.add(
'fslreorient2std',
fsl.utils.Reorient2Std(
output_type='NIFTI_GZ'),
inputs={
'in_file': ('series', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
reoriented = (reorient, 'out_file')
else:
reoriented = ('series', nifti_gz_format)
# Denoise the dwi-scan
if self.branch('preproc_denoise'):
# Run denoising
denoise = pipeline.add(
'denoise',
DWIDenoise(),
inputs={
'in_file': reoriented},
requirements=[mrtrix_req.v('3.0rc3')])
# Calculate residual noise
subtract_operands = pipeline.add(
'subtract_operands',
Merge(2),
inputs={
'in1': reoriented,
'in2': (denoise, 'noise')})
pipeline.add(
'subtract',
MRCalc(
operation='subtract'),
inputs={
'operands': (subtract_operands, 'out')},
outputs={
'noise_residual': ('out_file', mrtrix_image_format)},
requirements=[mrtrix_req.v('3.0rc3')])
denoised = (denoise, 'out_file')
else:
denoised = reoriented
# Preproc kwargs
preproc_kwargs = {}
preproc_inputs = {'in_file': denoised,
'grad_fsl': gradients}
if self.provided('reverse_phase'):
if self.provided('magnitude', default_okay=False):
dwi_reference = ('magnitude', mrtrix_image_format)
else:
# Extract b=0 volumes
dwiextract = pipeline.add(
'dwiextract',
ExtractDWIorB0(
bzero=True,
out_ext='.nii.gz'),
inputs={
'in_file': denoised,
'fslgrad': gradients},
requirements=[mrtrix_req.v('3.0rc3')])
# Get first b=0 from dwi b=0 volumes
extract_first_b0 = pipeline.add(
"extract_first_vol",
MRConvert(
coord=(3, 0)),
inputs={
'in_file': (dwiextract, 'out_file')},
requirements=[mrtrix_req.v('3.0rc3')])
dwi_reference = (extract_first_b0, 'out_file')
# Concatenate extracted forward rpe with reverse rpe
combined_images = pipeline.add(
'combined_images',
MRCat(),
inputs={
'first_scan': dwi_reference,
'second_scan': ('reverse_phase', mrtrix_image_format)},
requirements=[mrtrix_req.v('3.0rc3')])
# Create node to assign the right PED to the diffusion
prep_dwi = pipeline.add(
'prepare_dwi',
PrepareDWI(),
inputs={
'pe_dir': ('ped', float),
'ped_polarity': ('pe_angle', float)})
preproc_kwargs['rpe_pair'] = True
distortion_correction = True
preproc_inputs['se_epi'] = (combined_images, 'out_file')
else:
distortion_correction = False
preproc_kwargs['rpe_none'] = True
if self.parameter('preproc_pe_dir') is not None:
preproc_kwargs['pe_dir'] = self.parameter('preproc_pe_dir')
preproc = pipeline.add(
'dwipreproc',
DWIPreproc(
no_clean_up=True,
out_file_ext='.nii.gz',
# FIXME: Need to determine this programmatically
# eddy_parameters = '--data_is_shelled '
temp_dir='dwipreproc_tempdir',
**preproc_kwargs),
inputs=preproc_inputs,
outputs={
'eddy_par': ('eddy_parameters', eddy_par_format)},
requirements=[mrtrix_req.v('3.0rc3'), fsl_req.v('5.0.10')],
wall_time=60)
if distortion_correction:
pipeline.connect(prep_dwi, 'pe', preproc, 'pe_dir')
mask = pipeline.add(
'dwi2mask',
BrainMask(
out_file='brainmask.nii.gz'),
inputs={
'in_file': (preproc, 'out_file'),
'grad_fsl': gradients},
requirements=[mrtrix_req.v('3.0rc3')])
# Create bias correct node
pipeline.add(
"bias_correct",
DWIBiasCorrect(
method='ants'),
inputs={
'grad_fsl': gradients, # internal
'in_file': (preproc, 'out_file'),
'mask': (mask, 'out_file')},
outputs={
'series_preproc': ('out_file', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3'), ants_req.v('2.0')])
return pipeline
def brain_extraction_pipeline(self, **name_maps):
"""
Generates a whole brain mask using MRtrix's 'dwi2mask' command
Parameters
----------
mask_tool: Str
Can be either 'bet' or 'dwi2mask' depending on which mask tool you
want to use
"""
if self.branch('bet_method', 'mrtrix'):
pipeline = self.new_pipeline(
'brain_extraction',
desc="Generate brain mask from b0 images",
citations=[mrtrix_cite],
name_maps=name_maps)
if self.provided('coreg_ref'):
series = 'series_coreg'
else:
series = 'series_preproc'
# Create mask node
masker = pipeline.add(
'dwi2mask',
BrainMask(
out_file='brain_mask.nii.gz'),
inputs={
'in_file': (series, nifti_gz_format),
'grad_fsl': self.fsl_grads(pipeline, coregistered=False)},
outputs={
'brain_mask': ('out_file', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
merge = pipeline.add(
'merge_operands',
Merge(2),
inputs={
'in1': ('mag_preproc', nifti_gz_format),
'in2': (masker, 'out_file')})
pipeline.add(
'apply_mask',
MRCalc(
operation='multiply'),
inputs={
'operands': (merge, 'out')},
outputs={
'brain': ('out_file', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
else:
pipeline = super().brain_extraction_pipeline(**name_maps)
return pipeline
def series_coreg_pipeline(self, **name_maps):
pipeline = super().series_coreg_pipeline(**name_maps)
# Apply coregistration transform to gradients
pipeline.add(
'transform_grads',
TransformGradients(),
inputs={
'gradients': ('grad_dirs', fsl_bvecs_format),
'transform': ('coreg_fsl_mat', text_matrix_format)},
outputs={
'grad_dirs_coreg': ('transformed', fsl_bvecs_format)})
return pipeline
def intensity_normalisation_pipeline(self, **name_maps):
if self.num_sessions < 2:
raise ArcanaMissingDataException(
"Cannot normalise intensities of DWI images as study only "
"contains a single session")
elif self.num_sessions < self.RECOMMENDED_NUM_SESSIONS_FOR_INTENS_NORM:
logger.warning(
"The number of sessions in the study ({}) is less than the "
"recommended number for intensity normalisation ({}). The "
"results may be unreliable".format(
self.num_sessions,
self.RECOMMENDED_NUM_SESSIONS_FOR_INTENS_NORM))
pipeline = self.new_pipeline(
name='intensity_normalization',
desc="Corrects for B1 field inhomogeneity",
citations=[mrtrix_req.v('3.0rc3')],
name_maps=name_maps)
mrconvert = pipeline.add(
'mrconvert',
MRConvert(
out_ext='.mif'),
inputs={
'in_file': (self.series_preproc_spec_name, nifti_gz_format),
'grad_fsl': self.fsl_grads(pipeline)},
requirements=[mrtrix_req.v('3.0rc3')])
# Pair subject and visit ids together, expanding so they can be
# joined and chained together
session_ids = pipeline.add(
'session_ids',
utility.IdentityInterface(
['subject_id', 'visit_id']),
inputs={
'subject_id': (Study.SUBJECT_ID, int),
'visit_id': (Study.VISIT_ID, int)})
# Set up join nodes
join_fields = ['dwis', 'masks', 'subject_ids', 'visit_ids']
join_over_subjects = pipeline.add(
'join_over_subjects',
utility.IdentityInterface(
join_fields),
inputs={
'masks': (self.brain_mask_spec_name, nifti_gz_format),
'dwis': (mrconvert, 'out_file'),
'subject_ids': (session_ids, 'subject_id'),
'visit_ids': (session_ids, 'visit_id')},
joinsource=self.SUBJECT_ID,
joinfield=join_fields)
join_over_visits = pipeline.add(
'join_over_visits',
Chain(
join_fields),
inputs={
'dwis': (join_over_subjects, 'dwis'),
'masks': (join_over_subjects, 'masks'),
'subject_ids': (join_over_subjects, 'subject_ids'),
'visit_ids': (join_over_subjects, 'visit_ids')},
joinsource=self.VISIT_ID,
joinfield=join_fields)
# Intensity normalization
intensity_norm = pipeline.add(
'dwiintensitynorm',
DWIIntensityNorm(),
inputs={
'in_files': (join_over_visits, 'dwis'),
'masks': (join_over_visits, 'masks')},
outputs={
'norm_intens_fa_template': ('fa_template',
mrtrix_image_format),
'norm_intens_wm_mask': ('wm_mask', mrtrix_image_format)},
requirements=[mrtrix_req.v('3.0rc3')])
# Set up expand nodes
pipeline.add(
'expand', SelectSession(),
inputs={
'subject_ids': (join_over_visits, 'subject_ids'),
'visit_ids': (join_over_visits, 'visit_ids'),
'inlist': (intensity_norm, 'out_files'),
'subject_id': (Study.SUBJECT_ID, int),
'visit_id': (Study.VISIT_ID, int)},
outputs={
'norm_intensity': ('item', mrtrix_image_format)})
# Connect inputs
return pipeline
def tensor_pipeline(self, **name_maps):
"""
Fits the apparrent diffusion tensor (DT) to each voxel of the image
"""
pipeline = self.new_pipeline(
name='tensor',
desc=("Estimates the apparent diffusion tensor in each "
"voxel"),
citations=[],
name_maps=name_maps)
# Create tensor fit node
pipeline.add(
'dwi2tensor',
FitTensor(
out_file='dti.nii.gz'),
inputs={
'grad_fsl': self.fsl_grads(pipeline),
'in_file': (self.series_preproc_spec_name, nifti_gz_format),
'in_mask': (self.brain_mask_spec_name, nifti_gz_format)},
outputs={
'tensor': ('out_file', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
return pipeline
def tensor_metrics_pipeline(self, **name_maps):
"""
Fits the apparrent diffusion tensor (DT) to each voxel of the image
"""
pipeline = self.new_pipeline(
name='fa',
desc=("Calculates the FA and ADC from a tensor image"),
citations=[],
name_maps=name_maps)
# Create tensor fit node
pipeline.add(
'metrics',
TensorMetrics(
out_fa='fa.nii.gz',
out_adc='adc.nii.gz'),
inputs={
'in_file': ('tensor', nifti_gz_format),
'in_mask': (self.brain_mask_spec_name, nifti_gz_format)},
outputs={
'fa': ('out_fa', nifti_gz_format),
'adc': ('out_adc', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
return pipeline
def response_pipeline(self, **name_maps):
"""
Estimates the fibre orientation distribution (FOD) using constrained
spherical deconvolution
Parameters
----------
response_algorithm : str
Algorithm used to estimate the response
"""
pipeline = self.new_pipeline(
name='response',
desc=("Estimates the fibre response function"),
citations=[mrtrix_cite],
name_maps=name_maps)
# Create fod fit node
response = pipeline.add(
'response',
ResponseSD(
algorithm=self.parameter('response_algorithm')),
inputs={
'grad_fsl': self.fsl_grads(pipeline),
'in_file': (self.series_preproc_spec_name, nifti_gz_format),
'in_mask': (self.brain_mask_spec_name, nifti_gz_format)},
outputs={
'wm_response': ('wm_file', text_format)},
requirements=[mrtrix_req.v('3.0rc3')])
# Connect to outputs
if self.multi_tissue:
response.inputs.gm_file = 'gm.txt',
response.inputs.csf_file = 'csf.txt',
pipeline.connect_output('gm_response', response, 'gm_file',
text_format)
pipeline.connect_output('csf_response', response, 'csf_file',
text_format)
return pipeline
def average_response_pipeline(self, **name_maps):
"""
Averages the estimate response function over all subjects in the
project
"""
pipeline = self.new_pipeline(
name='average_response',
desc=(
"Averages the fibre response function over the project"),
citations=[mrtrix_cite],
name_maps=name_maps)
join_subjects = pipeline.add(
'join_subjects',
utility.IdentityInterface(['responses']),
inputs={
'responses': ('wm_response', text_format)},
outputs={},
joinsource=self.SUBJECT_ID,
joinfield=['responses'])
join_visits = pipeline.add(
'join_visits',
Chain(['responses']),
inputs={
'responses': (join_subjects, 'responses')},
joinsource=self.VISIT_ID,
joinfield=['responses'])
pipeline.add(
'avg_response',
AverageResponse(),
inputs={
'in_files': (join_visits, 'responses')},
outputs={
'avg_response': ('out_file', text_format)},
requirements=[mrtrix_req.v('3.0rc3')])
return pipeline
def fod_pipeline(self, **name_maps):
"""
Estimates the fibre orientation distribution (FOD) using constrained
spherical deconvolution
Parameters
----------
"""
pipeline = self.new_pipeline(
name='fod',
desc=("Estimates the fibre orientation distribution in each"
" voxel"),
citations=[mrtrix_cite],
name_maps=name_maps)
# Create fod fit node
dwi2fod = pipeline.add(
'dwi2fod',
EstimateFOD(
algorithm=self.parameter('fod_algorithm')),
inputs={
'in_file': (self.series_preproc_spec_name, nifti_gz_format),
'wm_txt': ('wm_response', text_format),
'mask_file': (self.brain_mask_spec_name, nifti_gz_format),
'grad_fsl': self.fsl_grads(pipeline)},
outputs={
'wm_odf': ('wm_odf', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
if self.multi_tissue:
dwi2fod.inputs.gm_odf = 'gm.mif',
dwi2fod.inputs.csf_odf = 'csf.mif',
pipeline.connect_input('gm_response', dwi2fod, 'gm_txt',
text_format),
pipeline.connect_input('csf_response', dwi2fod, 'csf_txt',
text_format),
pipeline.connect_output('gm_odf', dwi2fod, 'gm_odf',
nifti_gz_format),
pipeline.connect_output('csf_odf', dwi2fod, 'csf_odf',
nifti_gz_format),
# Check inputs/output are connected
return pipeline
def extract_b0_pipeline(self, **name_maps):
"""
Extracts the b0 images from a DWI study and takes their mean
"""
pipeline = self.new_pipeline(
name='extract_b0',
desc="Extract b0 image from a DWI study",
citations=[mrtrix_cite],
name_maps=name_maps)
# Extraction node
extract_b0s = pipeline.add(
'extract_b0s',
ExtractDWIorB0(
bzero=True,
quiet=True),
inputs={
'fslgrad': self.fsl_grads(pipeline),
'in_file': (self.series_preproc_spec_name, nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
# FIXME: Need a registration step before the mean
# Mean calculation node
mean = pipeline.add(
"mean",
MRMath(
axis=3,
operation='mean',
quiet=True),
inputs={
'in_files': (extract_b0s, 'out_file')},
requirements=[mrtrix_req.v('3.0rc3')])
# Convert to Nifti
pipeline.add(
"output_conversion",
MRConvert(
out_ext='.nii.gz',
quiet=True),
inputs={
'in_file': (mean, 'out_file')},
outputs={
'b0': ('out_file', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
return pipeline
def global_tracking_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='global_tracking',
desc="Extract b0 image from a DWI study",
citations=[mrtrix_cite],
name_maps=name_maps)
mask = pipeline.add(
'mask',
DWI2Mask(),
inputs={
'grad_fsl': self.fsl_grads(pipeline),
'in_file': (self.series_preproc_spec_name, nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
tracking = pipeline.add(
'tracking',
Tractography(
select=self.parameter('num_global_tracks'),
cutoff=self.parameter('global_tracks_cutoff')),
inputs={
'seed_image': (mask, 'out_file'),
'in_file': ('wm_odf', mrtrix_image_format)},
outputs={
'global_tracks': ('out_file', mrtrix_track_format)},
requirements=[mrtrix_req.v('3.0rc3')])
if self.provided('anat_5tt'):
pipeline.connect_input('anat_5tt', tracking, 'act_file',
mrtrix_image_format)
return pipeline
def intrascan_alignment_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='affine_mat_generation',
desc=("Generation of the affine matrices for the main dwi "
"sequence starting from eddy motion parameters"),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
'gen_aff_mats',
AffineMatrixGeneration(),
inputs={
'reference_image': ('mag_preproc', nifti_gz_format),
'motion_parameters': ('eddy_par', eddy_par_format)},
outputs={
'align_mats': ('affine_matrices', motion_mats_format)})
return pipeline
def connectome_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='connectome',
desc=("Generate a connectome from whole brain connectivity"),
citations=[],
name_maps=name_maps)
aseg_path = pipeline.add(
'aseg_path',
AppendPath(
sub_paths=['mri', 'aparc+aseg.mgz']),
inputs={
'base_path': ('anat_fs_recon_all', directory_format)})
pipeline.add(
'connectome',
mrtrix3.BuildConnectome(),
inputs={
'in_file': ('global_tracks', mrtrix_track_format),
'in_parc': (aseg_path, 'out_path')},
outputs={
'connectome': ('out_file', csv_format)},
requirements=[mrtrix_req.v('3.0rc3')])
return pipeline
class EpiStudy(MriStudy, metaclass=StudyMetaClass):
add_data_specs = [
InputFilesetSpec('coreg_ref_wmseg', STD_IMAGE_FORMATS,
optional=True),
InputFilesetSpec('field_map_mag', STD_IMAGE_FORMATS,
optional=True),
InputFilesetSpec('field_map_phase', STD_IMAGE_FORMATS,
optional=True),
FieldSpec('field_map_delta_te', float,
'field_map_time_info_pipeline')]
add_param_specs = [
SwitchSpec('bet_robust', True),
ParamSpec('bet_f_threshold', 0.2),
ParamSpec('bet_reduce_bias', False),
ParamSpec('fugue_echo_spacing', 0.000275)]
def preprocess_pipeline(self, **name_maps):
if ('field_map_phase' in self.input_names and
'field_map_mag' in self.input_names):
return self._fugue_pipeline(**name_maps)
else:
return super().preprocess_pipeline(**name_maps)
def _fugue_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='preprocess_pipeline',
desc=("Fugue distortion correction pipeline"),
citations=[fsl_cite],
name_maps=name_maps)
reorient_epi_in = pipeline.add(
'reorient_epi_in',
fsl.utils.Reorient2Std(
output_type='NIFTI_GZ'),
inputs={
'in_file': ('magnitude', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
fm_mag_reorient = pipeline.add(
'reorient_fm_mag',
fsl.utils.Reorient2Std(
output_type='NIFTI_GZ'),
inputs={
'in_file': ('field_map_mag', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
fm_phase_reorient = pipeline.add(
'reorient_fm_phase',
fsl.utils.Reorient2Std(
output_type='NIFTI_GZ'),
inputs={
'in_file': ('field_map_phase', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
bet = pipeline.add(
"bet",
BET(
robust=True,
output_type='NIFTI_GZ'),
inputs={
'in_file': (fm_mag_reorient, 'out_file')},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
create_fmap = pipeline.add(
"prepfmap",
PrepareFieldmap(
# delta_TE=2.46
),
inputs={
'delta_TE': ('field_map_delta_te', float),
"in_magnitude": (bet, "out_file"),
'in_phase': (fm_phase_reorient, 'out_file')},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
pipeline.add(
'fugue',
FUGUE(
unwarp_direction='x',
dwell_time=self.parameter('fugue_echo_spacing'),
unwarped_file='example_func.nii.gz',
output_type='NIFTI_GZ'),
inputs={
'fmap_in_file': (create_fmap, 'out_fieldmap'),
'in_file': (reorient_epi_in, 'out_file')},
outputs={
'mag_preproc': ('unwarped_file', nifti_gz_format)},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
return pipeline
def field_map_time_info_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='field_map_time_info_pipeline',
desc=("Pipeline to extract delta TE from field map "
"images, if provided"),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add(
'extract_delta_te',
FieldMapTimeInfo(),
inputs={
'fm_mag': ('field_map_mag', dicom_format)},
outputs={
'field_map_delta_te': ('delta_te', float)})
return pipeline
def create_motion_correction_class(name,
ref=None,
ref_type=None,
t1s=None,
t2s=None,
dwis=None,
epis=None,
umap=None,
dynamic=False,
umap_ref=None,
pet_data_dir=None,
pet_recon_dir=None,
struct2align=None):
inputs = []
dct = {}
data_specs = []
run_pipeline = False
param_specs = [ParamSpec('ref_resampled_resolution', [1])]
switch_specs = []
if struct2align is not None:
struct_image = struct2align.split('/')[-1].split('.')[0]
if pet_data_dir is not None:
inputs.append(
InputFilesets('pet_data_dir', 'pet_data_dir', directory_format))
if pet_recon_dir is not None:
inputs.append(
InputFilesets('pet_data_reconstructed', 'pet_data_reconstructed',
directory_format))
if struct2align is not None:
inputs.append(
InputFilesets('struct2align', struct_image, nifti_gz_format))
if pet_data_dir is not None and pet_recon_dir is not None and dynamic:
output_data = 'dynamic_motion_correction_results'
param_specs.append(ParamSpec('dynamic_pet_mc', True))
if struct2align is not None:
inputs.append(
InputFilesets('struct2align', struct_image, nifti_gz_format))
elif (pet_recon_dir is not None and not dynamic):
output_data = 'static_motion_correction_results'
else:
output_data = 'motion_detection_output'
if not ref:
raise Exception('A reference image must be provided!')
if ref_type == 't1':
ref_study = T1Study
elif ref_type == 't2':
ref_study = T2Study
else:
raise Exception('{} is not a recognized ref_type!The available '
'ref_types are t1 or t2.'.format(ref_type))
study_specs = [SubStudySpec('ref', ref_study)]
ref_spec = {'ref_brain': 'coreg_ref_brain'}
inputs.append(InputFilesets('ref_primary', ref, dicom_format))
if umap_ref and umap:
if umap_ref.endswith('/'):
umap_ref = umap_ref.split('/')[-2]
else:
umap_ref = umap_ref.split('/')[-1]
if umap_ref in t1s:
umap_ref_study = T1Study
t1s.remove(umap_ref)
elif umap_ref in t2s:
umap_ref_study = T2Study
t2s.remove(umap_ref)
else:
umap_ref = None
if t1s:
study_specs.extend([
SubStudySpec('t1_{}'.format(i), T1Study, ref_spec)
for i in range(len(t1s))
])
inputs.extend(
InputFilesets('t1_{}_primary'.format(i), dicom_format, t1_scan)
for i, t1_scan in enumerate(t1s))
run_pipeline = True
if t2s:
study_specs.extend([
SubStudySpec('t2_{}'.format(i), T2Study, ref_spec)
for i in range(len(t2s))
])
inputs.extend(
InputFilesets('t2_{}_primary'.format(i), t2_scan, dicom_format)
for i, t2_scan in enumerate(t2s))
run_pipeline = True
if umap_ref and not umap:
logger.info(
'Umap not provided. The umap realignment will not be '
'performed. Umap_ref will be trated as {}'.format(umap_ref_study))
elif umap_ref and umap:
logger.info('Umap will be realigned to match the head position in '
'each frame.')
if type(umap) == list and len(umap) > 1:
logger.info('More than one umap provided. Only the first one will '
'be used.')
umap = umap[0]
study_specs.append(SubStudySpec('umap_ref', umap_ref_study, ref_spec))
inputs.append(InputFilesets('umap_ref_primary', dicom_format,
umap_ref))
inputs.append(InputFilesets('umap', dicom_format, umap))
run_pipeline = True
elif not umap_ref and umap:
logger.warning('Umap provided without corresponding reference image. '
'Realignment cannot be performed without umap_ref. Umap'
' will be ignored.')
if epis:
epi_refspec = ref_spec.copy()
epi_refspec.update({
'ref_wm_seg': 'coreg_ref_wmseg',
'ref_preproc': 'coreg_ref'
})
study_specs.extend(
SubStudySpec('epi_{}'.format(i), EpiSeriesStudy, epi_refspec)
for i in range(len(epis)))
inputs.extend(
InputFilesets('epi_{}_primary'.format(i), epi_scan, dicom_format)
for i, epi_scan in enumerate(epis))
run_pipeline = True
if dwis:
unused_dwi = []
dwis_main = [x for x in dwis if x[-1] == '0']
dwis_ref = [x for x in dwis if x[-1] == '1']
dwis_opposite = [x for x in dwis if x[-1] == '-1']
dwi_refspec = ref_spec.copy()
dwi_refspec.update({
'ref_wm_seg': 'coreg_ref_wmseg',
'ref_preproc': 'coreg_ref'
})
if dwis_main:
switch_specs.extend(
SwitchSpec('dwi_{}_brain_extract_method'.format(i), 'fsl', (
'mrtrix', 'fsl')) for i in range(len(dwis_main)))
if dwis_main and not dwis_opposite:
logger.warning(
'No opposite phase encoding direction b0 provided. DWI '
'motion correction will be performed without distortion '
'correction. THIS IS SUB-OPTIMAL!')
study_specs.extend(
SubStudySpec('dwi_{}'.format(i), DwiStudy, dwi_refspec)
for i in range(len(dwis_main)))
inputs.extend(
InputFilesets('dwi_{}_primary'.format(i), dwis_main_scan[0],
dicom_format)
for i, dwis_main_scan in enumerate(dwis_main))
if dwis_main and dwis_opposite:
study_specs.extend(
SubStudySpec('dwi_{}'.format(i), DwiStudy, dwi_refspec)
for i in range(len(dwis_main)))
inputs.extend(
InputFilesets('dwi_{}_primary'.format(i), dwis_main[i][0],
dicom_format) for i in range(len(dwis_main)))
if len(dwis_main) <= len(dwis_opposite):
inputs.extend(
InputFilesets('dwi_{}_dwi_reference'.format(i),
dwis_opposite[i][0], dicom_format)
for i in range(len(dwis_main)))
else:
inputs.extend(
InputFilesets('dwi_{}_dwi_reference'.format(i),
dwis_opposite[0][0], dicom_format)
for i in range(len(dwis_main)))
if dwis_opposite and dwis_main and not dwis_ref:
study_specs.extend(
SubStudySpec('b0_{}'.format(i), EpiSeriesStudy, dwi_refspec)
for i in range(len(dwis_opposite)))
inputs.extend(
InputFilesets('b0_{}_primary'.format(i), dwis_opposite[i][0],
dicom_format) for i in range(len(dwis_opposite)))
if len(dwis_opposite) <= len(dwis_main):
inputs.extend(
InputFilesets('b0_{}_reverse_phase'.format(i), dwis_main[i]
[0], dicom_format)
for i in range(len(dwis_opposite)))
else:
inputs.extend(
InputFilesets('b0_{}_reverse_phase'.format(i), dwis_main[0]
[0], dicom_format)
for i in range(len(dwis_opposite)))
elif dwis_opposite and dwis_ref:
min_index = min(len(dwis_opposite), len(dwis_ref))
study_specs.extend(
SubStudySpec('b0_{}'.format(i), EpiSeriesStudy, dwi_refspec)
for i in range(min_index * 2))
inputs.extend(
InputFilesets('b0_{}_primary'.format(i), scan[0], dicom_format)
for i, scan in enumerate(dwis_opposite[:min_index] +
dwis_ref[:min_index]))
inputs.extend(
InputFilesets('b0_{}_reverse_phase'.format(i), scan[0],
dicom_format)
for i, scan in enumerate(dwis_ref[:min_index] +
dwis_opposite[:min_index]))
unused_dwi = [
scan
for scan in dwis_ref[min_index:] + dwis_opposite[min_index:]
]
elif dwis_opposite or dwis_ref:
unused_dwi = [scan for scan in dwis_ref + dwis_opposite]
if unused_dwi:
logger.info(
'The following scans:\n{}\nwere not assigned during the DWI '
'motion detection initialization (probably a different number '
'of main DWI scans and b0 images was provided). They will be '
'processed os "other" scans.'.format('\n'.join(
s[0] for s in unused_dwi)))
study_specs.extend(
SubStudySpec('t2_{}'.format(i), T2Study, ref_spec)
for i in range(len(t2s),
len(t2s) + len(unused_dwi)))
inputs.extend(
InputFilesets('t2_{}_primary'.format(i), scan[0], dicom_format)
for i, scan in enumerate(unused_dwi, start=len(t2s)))
run_pipeline = True
if not run_pipeline:
raise Exception('At least one scan, other than the reference, must be '
'provided!')
dct['add_substudy_specs'] = study_specs
dct['add_data_specs'] = data_specs
dct['__metaclass__'] = MultiStudyMetaClass
dct['add_param_specs'] = param_specs
dct['add_switch_specs'] = switch_specs
return (MultiStudyMetaClass(name, (MotionDetectionMixin, ),
dct), inputs, output_data)
class EpiSeriesStudy(MriStudy, metaclass=StudyMetaClass):
add_data_specs = [
InputFilesetSpec('series',
STD_IMAGE_FORMATS,
desc=("The set of EPI volumes that make up the "
"series")),
InputFilesetSpec('coreg_ref_wmseg', STD_IMAGE_FORMATS, optional=True),
InputFilesetSpec('reverse_phase', STD_IMAGE_FORMATS, optional=True),
InputFilesetSpec('field_map_mag', STD_IMAGE_FORMATS, optional=True),
InputFilesetSpec('field_map_phase', STD_IMAGE_FORMATS, optional=True),
FilesetSpec('magnitude',
nifti_gz_format,
'extract_magnitude_pipeline',
desc=("The magnitude image, typically extracted from "
"the provided series")),
FilesetSpec('series_preproc', nifti_gz_format, 'preprocess_pipeline'),
FilesetSpec('series_coreg', nifti_gz_format, 'series_coreg_pipeline'),
FilesetSpec('moco', nifti_gz_format, 'intrascan_alignment_pipeline'),
FilesetSpec('align_mats', motion_mats_format,
'intrascan_alignment_pipeline'),
FilesetSpec('moco_par', par_format, 'intrascan_alignment_pipeline'),
FieldSpec('field_map_delta_te', float, 'field_map_time_info_pipeline')
]
add_param_specs = [
SwitchSpec('bet_robust', True),
MriStudy.param_spec('coreg_method').with_new_choices(
'epireg', fallbacks={'epireg': 'flirt'}),
ParamSpec('bet_f_threshold', 0.2),
ParamSpec('bet_reduce_bias', False),
ParamSpec('fugue_echo_spacing', 0.000275)
]
@property
def header_image_spec_name(self):
if self.provided('header_image'):
hdr_name = 'header_image'
else:
hdr_name = 'series'
return hdr_name
@property
def series_preproc_spec_name(self):
if self.is_coregistered:
preproc = 'series_coreg'
else:
preproc = 'series_preproc'
return preproc
def coreg_pipeline(self, **name_maps):
if self.branch('coreg_method', 'epireg'):
pipeline = self._epireg_linear_coreg_pipeline(**name_maps)
else:
pipeline = super().coreg_pipeline(**name_maps)
return pipeline
def _epireg_linear_coreg_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='linear_coreg',
desc=("Intra-subjects epi registration improved using white "
"matter boundaries."),
citations=[fsl_cite],
name_maps=name_maps)
epireg = pipeline.add('epireg',
fsl.epi.EpiReg(out_base='epireg2ref',
output_type='NIFTI_GZ'),
inputs={
'epi': ('brain', nifti_gz_format),
't1_brain':
('coreg_ref_brain', nifti_gz_format),
't1_head': ('coreg_ref', nifti_gz_format)
},
outputs={
'brain_coreg': ('out_file', nifti_gz_format),
'coreg_fsl_mat':
('epi2str_mat', text_matrix_format)
},
requirements=[fsl_req.v('5.0.9')])
if self.provided('coreg_ref_wmseg'):
pipeline.connect_input('coreg_ref_wmseg', epireg, 'wmseg',
nifti_gz_format)
return pipeline
def brain_coreg_pipeline(self, **name_maps):
if self.branch('coreg_method', 'epireg'):
pipeline = self.coreg_pipeline(
name='brain_coreg',
name_maps=dict(input_map={
'mag_preproc': 'brain',
'coreg_ref': 'coreg_ref_brain'
},
output_map={'mag_coreg': 'brain_coreg'},
name_maps=name_maps))
pipeline.add(
'mask_transform',
fsl.ApplyXFM(output_type='NIFTI_GZ', apply_xfm=True),
inputs={
'in_matrix_file': (pipeline.node('epireg'), 'epi2str_mat'),
'in_file': ('brain_mask', nifti_gz_format),
'reference': ('coreg_ref_brain', nifti_gz_format)
},
outputs={'brain_mask_coreg': ('out_file', nifti_gz_format)},
requirements=[fsl_req.v('5.0.10')],
wall_time=10)
else:
pipeline = super().coreg_brain_pipeline(**name_maps)
return pipeline
def extract_magnitude_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
'extract_magnitude',
desc="Extracts a single magnitude volume from a series",
citations=[],
name_maps=name_maps)
pipeline.add("extract_first_vol",
MRConvert(coord=(3, 0)),
inputs={'in_file': ('series', nifti_gz_format)},
outputs={'magnitude': ('out_file', nifti_gz_format)},
requirements=[mrtrix_req.v('3.0rc3')])
return pipeline
def series_coreg_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
'series_coreg',
desc="Applies coregistration transform to DW series",
citations=[],
name_maps=name_maps)
if self.provided('coreg_ref'):
coreg_ref = 'coreg_ref'
elif self.provided('coreg_ref_brain'):
coreg_ref = 'coreg_ref_brain'
else:
raise BananaUsageError(
"Cannot coregister DW series as reference ('coreg_ref' or "
"'coreg_ref_brain') has not been provided to {}".format(self))
# Apply co-registration transformation to DW series
pipeline.add('mask_transform',
fsl.ApplyXFM(output_type='NIFTI_GZ', apply_xfm=True),
inputs={
'in_matrix_file':
('coreg_fsl_mat', text_matrix_format),
'in_file': ('series_preproc', nifti_gz_format),
'reference': (coreg_ref, nifti_gz_format)
},
outputs={'series_coreg': ('out_file', nifti_gz_format)},
requirements=[fsl_req.v('5.0.10')],
wall_time=10)
return pipeline
def intrascan_alignment_pipeline(self, **name_maps):
pipeline = self.new_pipeline(name='MCFLIRT_pipeline',
desc=("Intra-epi volumes alignment."),
citations=[fsl_cite],
name_maps=name_maps)
mcflirt = pipeline.add(
'mcflirt',
fsl.MCFLIRT(ref_vol=0,
save_mats=True,
save_plots=True,
output_type='NIFTI_GZ',
out_file='moco.nii.gz'),
inputs={'in_file': ('mag_preproc', nifti_gz_format)},
outputs={
'moco': ('out_file', nifti_gz_format),
'moco_par': ('par_file', par_format)
},
requirements=[fsl_req.v('5.0.9')])
pipeline.add('merge',
MergeListMotionMat(),
inputs={'file_list': (mcflirt, 'mat_file')},
outputs={'align_mats': ('out_dir', motion_mats_format)})
return pipeline
def field_map_time_info_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='field_map_time_info_pipeline',
desc=("Pipeline to extract delta TE from field map "
"images, if provided"),
citations=[fsl_cite],
name_maps=name_maps)
pipeline.add('extract_delta_te',
FieldMapTimeInfo(),
inputs={'fm_mag': ('field_map_mag', dicom_format)},
outputs={'field_map_delta_te': ('delta_te', float)})
return pipeline
def preprocess_pipeline(self, **name_maps):
if ('field_map_phase' in self.input_names
and 'field_map_mag' in self.input_names):
return self._fugue_pipeline(**name_maps)
elif 'reverse_phase' in self.input_names:
return self._topup_pipeline(**name_maps)
else:
return super().preprocess_pipeline(**name_maps)
def _topup_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='preprocess_pipeline',
desc=("Topup distortion correction pipeline"),
citations=[fsl_cite],
name_maps=name_maps)
reorient_epi_in = pipeline.add(
'reorient_epi_in',
fsl.utils.Reorient2Std(),
inputs={'in_file': ('series', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
reorient_epi_opposite = pipeline.add(
'reorient_epi_opposite',
fsl.utils.Reorient2Std(),
inputs={'in_file': ('reverse_phase', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
prep_dwi = pipeline.add('prepare_dwi',
PrepareDWI(topup=True),
inputs={
'pe_dir': ('ped', str),
'ped_polarity': ('pe_angle', str),
'dwi': (reorient_epi_in, 'out_file'),
'dwi1': (reorient_epi_opposite, 'out_file')
})
ped = pipeline.add('gen_config',
GenTopupConfigFiles(),
inputs={'ped': (prep_dwi, 'pe')})
merge_outputs = pipeline.add('merge_files',
merge_lists(2),
inputs={
'in1': (prep_dwi, 'main'),
'in2': (prep_dwi, 'secondary')
})
merge = pipeline.add('fsl_merge',
fsl_merge(dimension='t', output_type='NIFTI_GZ'),
inputs={'in_files': (merge_outputs, 'out')},
requirements=[fsl_req.v('5.0.9')])
topup = pipeline.add('topup',
TOPUP(output_type='NIFTI_GZ'),
inputs={
'in_file': (merge, 'merged_file'),
'encoding_file': (ped, 'config_file')
},
requirements=[fsl_req.v('5.0.9')])
in_apply_tp = pipeline.add(
'in_apply_tp',
merge_lists(1),
inputs={'in1': (reorient_epi_in, 'out_file')})
pipeline.add(
'applytopup',
ApplyTOPUP(method='jac', in_index=[1], output_type='NIFTI_GZ'),
inputs={
'in_files': (in_apply_tp, 'out'),
'encoding_file': (ped, 'apply_topup_config'),
'in_topup_movpar': (topup, 'out_movpar'),
'in_topup_fieldcoef': (topup, 'out_fieldcoef')
},
outputs={'series_preproc': ('out_corrected', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
return pipeline
def _fugue_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='preprocess_pipeline',
desc=("Fugue distortion correction pipeline"),
citations=[fsl_cite],
name_maps=name_maps)
reorient_epi_in = pipeline.add(
'reorient_epi_in',
fsl.utils.Reorient2Std(output_type='NIFTI_GZ'),
inputs={'in_file': ('series', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
fm_mag_reorient = pipeline.add(
'reorient_fm_mag',
fsl.utils.Reorient2Std(output_type='NIFTI_GZ'),
inputs={'in_file': ('field_map_mag', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
fm_phase_reorient = pipeline.add(
'reorient_fm_phase',
fsl.utils.Reorient2Std(output_type='NIFTI_GZ'),
inputs={'in_file': ('field_map_phase', nifti_gz_format)},
requirements=[fsl_req.v('5.0.9')])
bet = pipeline.add("bet",
BET(robust=True, output_type='NIFTI_GZ'),
inputs={'in_file': (fm_mag_reorient, 'out_file')},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
create_fmap = pipeline.add(
"prepfmap",
PrepareFieldmap(
# delta_TE=2.46
),
inputs={
'delta_TE': ('field_map_delta_te', float),
"in_magnitude": (bet, "out_file"),
'in_phase': (fm_phase_reorient, 'out_file')
},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
pipeline.add(
'fugue',
FUGUE(unwarp_direction='x',
dwell_time=self.parameter('fugue_echo_spacing'),
unwarped_file='example_func.nii.gz',
output_type='NIFTI_GZ'),
inputs={
'fmap_in_file': (create_fmap, 'out_fieldmap'),
'in_file': (reorient_epi_in, 'out_file')
},
outputs={'series_preproc': ('unwarped_file', nifti_gz_format)},
wall_time=5,
requirements=[fsl_req.v('5.0.9')])
return pipeline
def motion_mat_pipeline(self, **name_maps):
pipeline = self.new_pipeline(name='motion_mat_calculation',
desc=("Motion matrices calculation"),
citations=[fsl_cite],
name_maps=name_maps)
mm = pipeline.add(
'motion_mats',
MotionMatCalculation(),
inputs={
'reg_mat': ('coreg_fsl_mat', text_matrix_format),
'qform_mat': ('qform_mat', text_matrix_format)
},
outputs={'motion_mats': ('motion_mats', motion_mats_format)})
if 'reverse_phase' not in self.input_names:
pipeline.connect_input('align_mats', mm, 'align_mats',
motion_mats_format)
return pipeline