def create(self):
trainT1s = Node(interface=Select(), name='trainT1s')
trainT2s = Node(interface=Select(), name='trainT2s')
trainLabels = Node(interface=Select(), name='trainLabels')
testT1s = Node(interface=Select(), name='testT1s')
#intensityImages = Node(interface=Merge(2), name='intensityImages')
jointFusion = Node(interface=JointFusion(), name='jointFusion')
jointFusion.inputs.num_threads = -1
jointFusion.inputs.dimension = 3
jointFusion.inputs.modalities = 1 #TODO: verify 2 for T1/T2
jointFusion.inputs.method = "Joint[0.1,2]" # this does not work
jointFusion.inputs.output_label_image = 'fusion_neuro2012_20.nii.gz'
outputs = Node(
interface=IdentityInterface(fields=['output_label_image']),
run_without_submitting=True,
name='outputspec')
self.connect([ # Don't worry about T2s now per Regina
# (trainT1s, intensityImages, [('out', 'in1')]),
# (trainT2s, intensityImages, [('out', 'in2')]),
(testT1s, jointFusion, [('out', 'target_image')]),
(trainT1s, jointFusion, [('out', 'warped_intensity_images')]),
(trainLabels, jointFusion, [('out', 'warped_label_images')]),
(jointFusion, outputs, [('output_label_image',
'output_label_image')]),
])
def workflow(filename, outputType, name):
seedworkflow = pipe.Workflow(name=name)
labels, seeds = getAtlasPoints(filename) # Create seed points
seedsIdentity = pipe.Node(interface=IdentityInterface(fields=['index']), name='seedsIdentity')
seedsIdentity.iterables = ('index', range(len(labels)))
selectSeed = pipe.Node(interface=Select(), name='selectSeed')
selectSeed.inputs.inlist = seeds
selectLabel = pipe.Node(interface=Select(), name='selectLabel')
selectLabel.inputs.inlist = labels
points = pipe.Node(interface=Function(function=createSphereExpression,
input_names=['coordinates', 'radius'],
output_names=['expression']),
name='createSphereExpression')
spheres = pipe.Node(interface=Calc(letters=['a']), name='afni3Dcalc_seeds')
spheres.inputs.outputtype = outputType
spheres.inputs.args = '-nscale'
seedworkflow.connect([(seedsIdentity, selectSeed, [('index', 'index')]),
(seedsIdentity, selectLabel, [('index', 'index')]),
(selectSeed, points, [('out', 'coordinates')]),
(points, spheres, [('expression', 'expr')])])
return seedworkflow
def test_Select_outputs():
output_map = dict(out=dict(),
)
outputs = Select.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def create(self):
sampleT1s = Node(interface=Select(), name='sampleT1s')
sampleT2s = Node(interface=Select(), name='sampleT2s')
sampleLabels = Node(interface=Select(), name='sampleLabels')
testT1s = Node(interface=Select(), name='testT1s')
testT2s = Node(interface=Select(), name='testT2s')
testLabels = Node(interface=Select(), name='testLabels')
intensityImages = Node(interface=Merge(2), name='intensityImages')
jointFusion = Node(interface=JointFusion(), name='jointFusion')
jointFusion.inputs.dimension = 3
jointFusion.inputs.modalities = 1 #TODO: verify 2 for T1/T2
jointFusion.inputs.method = 'Joint[0.1, 2]'
jointFusion.inputs.output_label_image = 'fusion_neuro2012_20.nii.gz'
outputs = Node(
interface=IdentityInterface(fields=['output_label_image']),
run_without_submitting=True,
name='outputspec')
self.connect([ # Don't worry about T2s now per Regina
# (sampleT1s, intensityImages, [('out', 'in1')]),
# (sampleT2s, intensityImages, [('out', 'in2')]),
# (intensityImages, jointFusion, [('out', 'warped_intensity_images')]),
(sampleT1s, jointFusion, [('out', 'warped_intensity_images')]),
#END: per Regina
(sampleLabels, jointFusion, [('out', 'warped_label_images')]),
(jointFusion, outputs, [('output_label_image',
'output_label_image')]),
])
def test_Select_inputs():
input_map = dict(ignore_exception=dict(nohash=True,
usedefault=True,
),
index=dict(mandatory=True,
),
inlist=dict(mandatory=True,
),
)
inputs = Select.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def create(self):
"""
This function...
:param self:
:return:
"""
trainT1s = Node(interface=Select(), name="trainT1s")
trainT2s = Node(interface=Select(), name="trainT2s")
trainLabels = Node(interface=Select(), name="trainLabels")
testT1s = Node(interface=Select(), name="testT1s")
# intensityImages = Node(interface=Merge(2), name='intensityImages')
jointFusion = Node(interface=JointFusion(), name="jointFusion")
jointFusion.inputs.num_threads = -1
jointFusion.inputs.dimension = 3
jointFusion.inputs.modalities = 1 # TODO: verify 2 for T1/T2
jointFusion.inputs.method = "Joint[0.1,2]" # this does not work
jointFusion.inputs.output_label_image = "fusion_neuro2012_20.nii.gz"
outputs = Node(
interface=IdentityInterface(fields=["output_label_image"]),
run_without_submitting=True,
name="outputspec",
)
self.connect(
[ # Don't worry about T2s now per Regina
# (trainT1s, intensityImages, [('out', 'in1')]),
# (trainT2s, intensityImages, [('out', 'in2')]),
(testT1s, jointFusion, [("out", "target_image")]),
(trainT1s, jointFusion, [("out", "warped_intensity_images")]),
(trainLabels, jointFusion, [("out", "warped_label_images")]),
(jointFusion, outputs, [("output_label_image", "output_label_image")]),
]
)
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 petpvc_workflow(wf_name="petpvc"):
""" Run the PET pre-processing workflow against the gunzip_pet.in_file files.
It coregisters the reference_file and tissues to PET space, then applies PVC and grey matter normalization.
It does:
- SPM12 Coregister T1 and tisues to PET
- PVC the PET image in PET space
Parameters
----------
wf_name: str
Name of the workflow.
Nipype Inputs
-------------
pvc_input.in_file: traits.File
The raw NIFTI_GZ PET image file
pvc_input.reference_file: traits.File
The anatomical image in its native space. For registration reference.
pvc_input.tissues: list of traits.File
List of tissues files from the New Segment process. At least the first
3 tissues must be present.
Nipype outputs
--------------
pvc_output.coreg_ref: existing file
The coregistered reference_file image in PET space.
pvc_output.coreg_others: list of existing files
List of coregistered files from coreg_pet.apply_to_files
pvc_output.pvc_out: existing file
The output of the PETPVC process.
pvc_output.petpvc_mask: existing file
The mask built for the PETPVC.
pvc_output.brain_mask: existing file
A brain mask calculated with the tissues file.
pvc_output.gm_norm: existing file
The output of the grey matter intensity normalization process.
This is the last step in the PET signal correction.
Returns
-------
wf: nipype Workflow
"""
# fixed parameters of the NUK mMR
psf_fwhm = (4.3, 4.3, 4.3)
# specify input and output fields
in_fields = [
"in_file",
"reference_file",
"tissues",
]
out_fields = [
"coreg_ref",
"coreg_others",
"pvc_out",
"petpvc_mask",
"brain_mask",
"gm_norm",
]
# input
pet_input = setup_node(IdentityInterface(fields=in_fields,
mandatory_inputs=True),
name="pvc_input")
flat_list = pe.Node(Function(input_names=['list_of_lists'],
output_names=['out'],
function=flatten_list),
name='flatten_tissue_list')
# coreg pet
gunzip_pet = setup_node(Gunzip(), name="gunzip_pet")
coreg_pet = setup_node(spm_coregister(cost_function="mi"),
name="coreg_pet")
tissues_sel = setup_node(Select(index=[0, 1, 2]), name="tissues")
select_gm = setup_node(Select(index=[0]), name="select_gm")
pvc = setup_node(petpvc_cmd(fwhm_mm=psf_fwhm, pvc_method='RBV'),
name="pvc")
# output
pvc_output = setup_node(IdentityInterface(fields=out_fields),
name="pvc_output")
# workflow to create the mask
mask_wf = petpvc_mask(wf_name="petpvc_mask")
# workflow for intensity normalization
norm_wf = intensity_norm(wf_name="intensity_norm_gm")
# Create the workflow object
wf = pe.Workflow(name=wf_name)
wf.connect([
# inputs
(pet_input, gunzip_pet, [("in_file", "in_file")]),
(pet_input, tissues_sel, [("tissues", "inlist")]),
])
# check how to perform the registration, to decide how to build the pipeline
anat2pet = get_config_setting('registration.anat2pet', False)
if anat2pet:
wf.connect([
# inputs
(pet_input, coreg_pet, [("reference_file", "source")]),
# unzip to coregister the reference file (anatomical image) to PET space.
(gunzip_pet, coreg_pet, [("out_file", "target")]),
(tissues_sel, flat_list, [("out", "list_of_lists")]),
(flat_list, coreg_pet, [("out", "apply_to_files")]),
# the list of tissues to the mask wf and the GM for PET intensity normalization
(coreg_pet, select_gm, [("coregistered_files", "inlist")]),
(coreg_pet, mask_wf, [("coregistered_files",
"pvcmask_input.tissues")]),
# the PET in native space to PVC correction
(gunzip_pet, pvc, [("out_file", "in_file")]),
# the merged file with 4 tissues to PCV correction
(mask_wf, pvc, [("pvcmask_output.petpvc_mask", "mask_file")]),
# normalize voxel values of PET PVCed by demeaning it entirely by GM PET voxel values
(pvc, norm_wf, [("out_file", "intnorm_input.source")]),
(select_gm, norm_wf, [("out", "intnorm_input.mask")]),
# output
(coreg_pet, pvc_output, [("coregistered_source", "coreg_ref")]),
(coreg_pet, pvc_output, [("coregistered_files", "coreg_others")]),
(pvc, pvc_output, [("out_file", "pvc_out")]),
(mask_wf, pvc_output, [("pvcmask_output.brain_mask", "brain_mask")
]),
(mask_wf, pvc_output, [("pvcmask_output.petpvc_mask",
"petpvc_mask")]),
(norm_wf, pvc_output, [("intnorm_output.out_file", "gm_norm")]),
])
else: # PET to ANAT
wf.connect([
# inputs
(pet_input, coreg_pet, [("reference_file", "target")]),
# unzip PET image and set as a source to register it to anatomical space.
(gunzip_pet, coreg_pet, [("out_file", "source")]),
(tissues_sel, flat_list, [("out", "list_of_lists")]),
(flat_list, coreg_pet, [("out", "apply_to_files")]),
# the list of tissues to the mask wf and the GM for PET intensity normalization
(tissues_sel, select_gm, [("out", "inlist")]),
(flat_list, mask_wf, [("out", "pvcmask_input.tissues")]),
# the PET in ANAT space to PVC correction
(coreg_pet, pvc, [("coregistered_source", "in_file")]),
# the merged file with 4 tissues to PCV correction
(mask_wf, pvc, [("pvcmask_output.petpvc_mask", "mask_file")]),
# normalize voxel values of PET PVCed by demeaning it entirely by GM PET voxel values
(pvc, norm_wf, [("out_file", "intnorm_input.source")]),
(select_gm, norm_wf, [("out", "intnorm_input.mask")]),
# output
# TODO: coreg_ref should have a different name in this case
(coreg_pet, pvc_output, [("coregistered_source", "coreg_ref")]),
(coreg_pet, pvc_output, [("coregistered_files", "coreg_others")]),
(pvc, pvc_output, [("out_file", "pvc_out")]),
(mask_wf, pvc_output, [("pvcmask_output.brain_mask", "brain_mask")
]),
(mask_wf, pvc_output, [("pvcmask_output.petpvc_mask",
"petpvc_mask")]),
(norm_wf, pvc_output, [("intnorm_output.out_file", "gm_norm")]),
])
return wf
def fmri_cleanup_wf(wf_name="fmri_cleanup"):
""" Run the resting-state fMRI pre-processing workflow against the rest files in `data_dir`.
Tasks:
- Trim first 6 volumes of the rs-fMRI file.
- Slice Timing correction.
- Motion and nuisance correction.
- Calculate brain mask in fMRI space.
- Bandpass frequency filtering for resting-state fMRI.
- Smoothing.
- Tissue maps co-registration to fMRI space.
Parameters
----------
wf_name: str
Nipype Inputs
-------------
rest_input.in_file: traits.File
The resting-state fMRI file.
rest_input.anat: traits.File
Path to the high-contrast anatomical image.
rest_input.tissues: list of traits.File
Paths to the tissue segmentations in anatomical space.
Expected to have this order: GM, WM and CSF.
rest_input.highpass_sigma:traits.Float
Band pass timeseries filter higher bound in Hz.
rest_input.lowpass_sigma: traits.Float
Band pass timeseries filter lower bound in Hz.
Nipype Outputs
--------------
rest_output.smooth: traits.File
The isotropically smoothed time filtered nuisance corrected image.
rest_output.nuis_corrected: traits.File
The nuisance corrected fMRI file.
rest_output.motion_params: traits.File
The affine transformation file.
rest_output.time_filtered: traits.File
The bandpass time filtered fMRI file.
rest_output.epi_brain_mask: traits.File
An estimated brain mask from mean EPI volume.
rest_output.tissues_brain_mask: traits.File
A brain mask calculated from the addition of coregistered
GM, WM and CSF segmentation volumes from the anatomical
segmentation.
rest_output.tissues: list of traits.File
The tissues segmentation volume in fMRI space.
Expected to have this order: GM, WM and CSF.
rest_output.anat: traits.File
The T1w image in fMRI space.
rest_output.avg_epi: traits.File
The average EPI image in fMRI space after slice-time and motion correction.
rest_output.motion_regressors: traits.File
rest_output.compcor_regressors: traits.File
rest_output.art_displacement_files
One image file containing the voxel-displacement timeseries.
rest_output.art_intensity_files
One file containing the global intensity values determined from the brainmask.
rest_output.art_norm_files
One file containing the composite norm.
rest_output.art_outlier_files
One file containing a list of 0-based indices corresponding to outlier volumes.
rest_output.art_plot_files
One image file containing the detected outliers.
rest_output.art_statistic_files
One file containing information about the different types of artifacts and if design info is provided then
details of stimulus correlated motion and a listing or artifacts by event type.
Returns
-------
wf: nipype Workflow
"""
# Create the workflow object
wf = pe.Workflow(name=wf_name)
# specify input and output fields
in_fields = [
"in_file",
"anat",
"atlas_anat",
"coreg_target",
"tissues",
"lowpass_freq",
"highpass_freq",
]
out_fields = [
"motion_corrected",
"motion_params",
"tissues",
"anat",
"avg_epi",
"time_filtered",
"smooth",
"tsnr_file",
"epi_brain_mask",
"tissues_brain_mask",
"motion_regressors",
"compcor_regressors",
"gsr_regressors",
"nuis_corrected",
"art_displacement_files",
"art_intensity_files",
"art_norm_files",
"art_outlier_files",
"art_plot_files",
"art_statistic_files",
]
# input identities
rest_input = setup_node(IdentityInterface(fields=in_fields, mandatory_inputs=True),
name="rest_input")
# rs-fMRI preprocessing nodes
trim = setup_node(Trim(), name="trim")
stc_wf = auto_spm_slicetime()
realign = setup_node(nipy_motion_correction(), name='realign')
# average
average = setup_node(
Function(
function=mean_img,
input_names=["in_file"],
output_names=["out_file"],
imports=['from neuro_pypes.interfaces.nilearn import ni2file']
),
name='average_epi'
)
mean_gunzip = setup_node(Gunzip(), name="mean_gunzip")
# co-registration nodes
coreg = setup_node(spm_coregister(cost_function="mi"), name="coreg_fmri")
brain_sel = setup_node(Select(index=[0, 1, 2]), name="brain_sel")
# brain mask made with EPI
epi_mask = setup_node(ComputeMask(), name='epi_mask')
# brain mask made with the merge of the tissue segmentations
tissue_mask = setup_node(fsl.MultiImageMaths(), name='tissue_mask')
tissue_mask.inputs.op_string = "-add %s -add %s -abs -kernel gauss 4 -dilM -ero -kernel gauss 1 -dilM -bin"
tissue_mask.inputs.out_file = "tissue_brain_mask.nii.gz"
# select tissues
gm_select = setup_node(Select(index=[0]), name="gm_sel")
wmcsf_select = setup_node(Select(index=[1, 2]), name="wmcsf_sel")
# noise filter
noise_wf = rest_noise_filter_wf()
wm_select = setup_node(Select(index=[1]), name="wm_sel")
csf_select = setup_node(Select(index=[2]), name="csf_sel")
# bandpass filtering
bandpass = setup_node(
Function(
input_names=['files', 'lowpass_freq', 'highpass_freq', 'tr'],
output_names=['out_files'],
function=bandpass_filter
),
name='bandpass'
)
# smooth
smooth = setup_node(
Function(
function=smooth_img,
input_names=["in_file", "fwhm"],
output_names=["out_file"],
imports=['from neuro_pypes.interfaces.nilearn import ni2file']
),
name="smooth"
)
smooth.inputs.fwhm = get_config_setting('fmri_smooth.fwhm', default=8)
smooth.inputs.out_file = "smooth_std_{}.nii.gz".format(wf_name)
# output identities
rest_output = setup_node(IdentityInterface(fields=out_fields), name="rest_output")
# Connect the nodes
wf.connect([
# trim
(rest_input, trim, [("in_file", "in_file")]),
# slice time correction
(trim, stc_wf, [("out_file", "stc_input.in_file")]),
# motion correction
(stc_wf, realign, [("stc_output.timecorrected_files", "in_file")]),
# coregistration target
(realign, average, [("out_file", "in_file")]),
(average, mean_gunzip, [("out_file", "in_file")]),
(mean_gunzip, coreg, [("out_file", "target")]),
# epi brain mask
(average, epi_mask, [("out_file", "mean_volume")]),
# coregistration
(rest_input, coreg, [("anat", "source")]),
(rest_input, brain_sel, [("tissues", "inlist")]),
(brain_sel, coreg, [(("out", flatten_list), "apply_to_files")]),
# tissue brain mask
(coreg, gm_select, [("coregistered_files", "inlist")]),
(coreg, wmcsf_select, [("coregistered_files", "inlist")]),
(gm_select, tissue_mask, [(("out", flatten_list), "in_file")]),
(wmcsf_select, tissue_mask, [(("out", flatten_list), "operand_files")]),
# nuisance correction
(coreg, wm_select, [("coregistered_files", "inlist",)]),
(coreg, csf_select, [("coregistered_files", "inlist",)]),
(realign, noise_wf, [("out_file", "rest_noise_input.in_file",)]),
(tissue_mask, noise_wf, [("out_file", "rest_noise_input.brain_mask")]),
(wm_select, noise_wf, [(("out", flatten_list), "rest_noise_input.wm_mask")]),
(csf_select, noise_wf, [(("out", flatten_list), "rest_noise_input.csf_mask")]),
(realign, noise_wf, [("par_file", "rest_noise_input.motion_params",)]),
# temporal filtering
(noise_wf, bandpass, [("rest_noise_output.nuis_corrected", "files")]),
# (realign, bandpass, [("out_file", "files")]),
(stc_wf, bandpass, [("stc_output.time_repetition", "tr")]),
(rest_input, bandpass, [
("lowpass_freq", "lowpass_freq"),
("highpass_freq", "highpass_freq"),
]),
(bandpass, smooth, [("out_files", "in_file")]),
# output
(epi_mask, rest_output, [("brain_mask", "epi_brain_mask")]),
(tissue_mask, rest_output, [("out_file", "tissues_brain_mask")]),
(realign, rest_output, [
("out_file", "motion_corrected"),
("par_file", "motion_params"),
]),
(coreg, rest_output, [
("coregistered_files", "tissues"),
("coregistered_source", "anat"),
]),
(noise_wf, rest_output, [
("rest_noise_output.motion_regressors", "motion_regressors"),
("rest_noise_output.compcor_regressors", "compcor_regressors"),
("rest_noise_output.gsr_regressors", "gsr_regressors"),
("rest_noise_output.nuis_corrected", "nuis_corrected"),
("rest_noise_output.tsnr_file", "tsnr_file"),
("rest_noise_output.art_displacement_files", "art_displacement_files"),
("rest_noise_output.art_intensity_files", "art_intensity_files"),
("rest_noise_output.art_norm_files", "art_norm_files"),
("rest_noise_output.art_outlier_files", "art_outlier_files"),
("rest_noise_output.art_plot_files", "art_plot_files"),
("rest_noise_output.art_statistic_files", "art_statistic_files"),
]),
(average, rest_output, [("out_file", "avg_epi")]),
(bandpass, rest_output, [("out_files", "time_filtered")]),
(smooth, rest_output, [("out_file", "smooth")]),
])
return wf
def create_stage(stage_nr, workflow, inputs, inputs_nr_slices, slice_name):
"""
Don't use this directly, see build_workflow() instead.
Create an interpolation stage. Mutates the 'workflow' argument.
"""
# Selectors into 'inputs'
select_inputs = {}
for i in range(inputs_nr_slices):
fi = Function(input_names=['x', 'i'],
output_names=['out_file'],
function=select_function)
select_inputs[i] = pe.Node(interface=fi,
name='select_inputs_%s_%d_%d' % (
slice_name,
stage_nr,
i,
))
select_inputs[i].inputs.i = i
workflow.connect(inputs, 'out_files', select_inputs[i], 'x')
# Interpolations.
interp_nodes = []
for i in range(inputs_nr_slices - 1):
interp_node = pe.Node(interface=InterpolateBetweenSlices(),
name='interp_%s_%d_%08d' % (
slice_name,
stage_nr,
i,
))
select_node = pe.Node(interface=Select(index=[i, i + 1]),
name='select_%s_%d_%d_%d' % (
slice_name,
stage_nr,
i,
i + 1,
))
workflow.connect(inputs, 'out_files', select_node, 'inlist')
workflow.connect(select_node, 'out', interp_node, 'slices')
interp_node.inputs.level = stage_nr
interp_nodes.append(interp_node)
# Rename slices.
renamers = []
k = 0
rename = pe.Node(interface=Rename(),
name='rename_%s_%d_%08d' % (
slice_name,
stage_nr,
k,
))
rename.inputs.format_string = 'slice_%08d.npz' % k
workflow.connect(select_inputs[0], 'out_file', rename, 'in_file')
renamers.append(rename)
k += 1
for i in range(len(interp_nodes)):
rename = pe.Node(interface=Rename(),
name='rename_%s_%d_%08d' % (
slice_name,
stage_nr,
k,
))
rename.inputs.format_string = 'slice_%08d.npz' % k
workflow.connect(interp_nodes[i], 'interpolated_slice', rename,
'in_file')
renamers.append(rename)
k += 1
rename = pe.Node(interface=Rename(),
name='rename_%s_%d_%08d' % (
slice_name,
stage_nr,
k,
))
rename.inputs.format_string = 'slice_%08d.npz' % k
workflow.connect(select_inputs[i + 1], 'out_file', rename, 'in_file')
renamers.append(rename)
k += 1
# Could skip this unless we want to see intermediate steps.
datasink = pe.Node(nio.DataSink(),
name='sinker_%s_%d' % (
slice_name,
stage_nr,
))
for (i, rename) in enumerate(renamers):
workflow.connect(rename, 'out_file', datasink, 'slices.@%d' % i)
# If we want to do another stage, use the out_file's of renamers.
# We need a single node with an output 'out_files' consisting of each of the files.
merge_renamed_files = pe.Node(interface=Merge(len(renamers)),
name='merge_renamed_files_%s_%d' % (
slice_name,
stage_nr,
))
for (i, rename) in enumerate(renamers):
workflow.connect(rename, 'out_file', merge_renamed_files,
'in%d' % (i + 1))
# Now rename the output 'out' to 'out_files' so we can pass it in to a recursive
# call to this function.
out_to_out_files = pe.Node(interface=Function(input_names=['x'],
output_names=['out_files'],
function=identity_function),
name='out_to_out_files_%s_%d' % (
slice_name,
stage_nr,
))
workflow.connect(merge_renamed_files, 'out', out_to_out_files, 'x')
return out_to_out_files
# Transform Compositetransform to a warpfield to use it with CreateJacobian
# This caculates the warp field of both the affine and non affine transformations
# If you did then, then you have to add the intracranial volume as covariate
# That's why I am replacing it,
# calc_warp_field = Node(ants.ApplyTransforms(), name = 'Calc_Warp_Field')
# calc_warp_field.inputs.reference_image = study_based_template
# calc_warp_field.inputs.dimension = 3
# calc_warp_field.inputs.print_out_composite_warp_file = True
# calc_warp_field.inputs.output_image = 'Warp_Field.nii.gz'
#-----------------------------------------------------------------------------------------------------
# In[1]
# Here we just get the warp field
# Notice I changed reg_sub_to_temp.inputs.write_composite_transform to False
# So, it outputs the warpfield seperate from the affine transform
get_warp_field = Node(Select(), name='get_warp_field')
get_warp_field.inputs.index = [1]
#-----------------------------------------------------------------------------------------------------
# In[1]:
#Create jacobian determinant
jacobian = Node(ants.CreateJacobianDeterminantImage(),
name='Calculate_Jacobian_Determinant')
jacobian.inputs.imageDimension = 3
jacobian.inputs.outputImage = 'Jacobian.nii.gz'
#-----------------------------------------------------------------------------------------------------
# In[1]:
#Tissue segmentation
atropos = Node(ants.Atropos(), name='Atropos')
def ANTs_cortical_thickness(subject_list, directory):
#==============================================================
# Loading required packages
import nipype.interfaces.io as nio
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import own_nipype
from nipype.interfaces.ants.segmentation import antsCorticalThickness
from nipype.interfaces.ants import ApplyTransforms
from nipype.interfaces.ants import MultiplyImages
from nipype.interfaces.utility import Function
from nipype.interfaces.ants.visualization import ConvertScalarImageToRGB
from nipype.interfaces.ants.visualization import CreateTiledMosaic
from nipype.interfaces.utility import Select
from own_nipype import GM_DENSITY
from nipype import SelectFiles
import os
#====================================
# Defining the nodes for the workflow
# Getting the subject ID
infosource = pe.Node(
interface=util.IdentityInterface(fields=['subject_id']),
name='infosource')
infosource.iterables = ('subject_id', subject_list)
# Getting the relevant diffusion-weighted data
templates = dict(
T1=
'/imaging/jb07/CALM/CALM_BIDS/{subject_id}/anat/{subject_id}_T1w.nii.gz'
)
selectfiles = pe.Node(SelectFiles(templates), name="selectfiles")
selectfiles.inputs.base_directory = os.path.abspath(directory)
# Rigid alignment with the template space
T1_rigid_quickSyN = pe.Node(interface=own_nipype.ants_QuickSyN(
image_dimensions=3, transform_type='r'),
name='T1_rigid_quickSyN')
T1_rigid_quickSyN.inputs.fixed_image = '/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/T_template0.nii.gz'
# Cortical thickness calculation
corticalthickness = pe.Node(interface=antsCorticalThickness(),
name='corticalthickness')
corticalthickness.inputs.brain_probability_mask = '/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/T_template0_BrainCerebellumProbabilityMask.nii.gz'
corticalthickness.inputs.brain_template = '/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/T_template0.nii.gz'
corticalthickness.inputs.segmentation_priors = [
'/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/Priors2/priors1.nii.gz',
'/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/Priors2/priors2.nii.gz',
'/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/Priors2/priors3.nii.gz',
'/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/Priors2/priors4.nii.gz',
'/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/Priors2/priors5.nii.gz',
'/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/Priors2/priors6.nii.gz'
]
corticalthickness.inputs.extraction_registration_mask = '/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/T_template0_BrainCerebellumExtractionMask.nii.gz'
corticalthickness.inputs.t1_registration_template = '/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/T_template0_BrainCerebellum.nii.gz'
# Creating visualisations for quality control
converter = pe.Node(interface=ConvertScalarImageToRGB(), name='converter')
converter.inputs.dimension = 3
converter.inputs.colormap = 'cool'
converter.inputs.minimum_input = 0
converter.inputs.maximum_input = 5
mosaic_slicer = pe.Node(interface=CreateTiledMosaic(),
name='mosaic_slicer')
mosaic_slicer.inputs.pad_or_crop = 'mask'
mosaic_slicer.inputs.slices = '[4 ,mask , mask]'
mosaic_slicer.inputs.direction = 1
mosaic_slicer.inputs.alpha_value = 0.5
# Getting GM density images
gm_density = pe.Node(interface=GM_DENSITY(), name='gm_density')
sl = pe.Node(interface=Select(index=1), name='sl')
# Applying transformation
at = pe.Node(interface=ApplyTransforms(), name='at')
at.inputs.dimension = 3
at.inputs.reference_image = '/imaging/jb07/Atlases/OASIS/OASIS-30_Atropos_template/T_template0_BrainCerebellum.nii.gz'
at.inputs.interpolation = 'Linear'
at.inputs.default_value = 0
at.inputs.invert_transform_flags = False
# Multiplying the normalized image with Jacobian
multiply_images = pe.Node(interface=MultiplyImages(dimension=3),
name='multiply_images')
# Naming the output of multiply_image
def generate_filename(subject_id):
return subject_id + '_multiplied.nii.gz'
generate_filename = pe.Node(interface=Function(
input_names=["subject_id"],
output_names=["out_filename"],
function=generate_filename),
name='generate_filename')
#====================================
# Setting up the workflow
antsthickness = pe.Workflow(name='antsthickness')
antsthickness.connect(infosource, 'subject_id', selectfiles, 'subject_id')
antsthickness.connect(selectfiles, 'T1', T1_rigid_quickSyN, 'moving_image')
antsthickness.connect(infosource, 'subject_id', T1_rigid_quickSyN,
'output_prefix')
antsthickness.connect(T1_rigid_quickSyN, 'warped_image', corticalthickness,
'anatomical_image')
antsthickness.connect(infosource, 'subject_id', corticalthickness,
'out_prefix')
antsthickness.connect(corticalthickness, 'CorticalThickness', converter,
'input_image')
antsthickness.connect(converter, 'output_image', mosaic_slicer,
'rgb_image')
antsthickness.connect(corticalthickness, 'BrainSegmentationN4',
mosaic_slicer, 'input_image')
antsthickness.connect(corticalthickness, 'BrainExtractionMask',
mosaic_slicer, 'mask_image')
antsthickness.connect(corticalthickness, 'BrainSegmentationN4', gm_density,
'in_file')
antsthickness.connect(corticalthickness, 'BrainSegmentationPosteriors', sl,
'inlist')
antsthickness.connect(sl, 'out', gm_density, 'mask_file')
antsthickness.connect(corticalthickness, 'SubjectToTemplate1Warp', at,
'transforms')
antsthickness.connect(gm_density, 'out_file', at, 'input_image')
antsthickness.connect(corticalthickness, 'SubjectToTemplateLogJacobian',
multiply_images, 'second_input')
antsthickness.connect(corticalthickness,
'CorticalThicknessNormedToTemplate', multiply_images,
'first_input')
antsthickness.connect(infosource, 'subject_id', generate_filename,
'subject_id')
antsthickness.connect(generate_filename, 'out_filename', multiply_images,
'output_product_image')
#====================================
# Running the workflow
antsthickness.base_dir = os.path.abspath(directory)
antsthickness.write_graph()
antsthickness.run('PBSGraph')
def writeSeedFiles():
CACHE_DIR = 'seeds_CACHE'
RESULTS_DIR = 'seeds'
REWRITE_DATASINKS = True
nacAtlasFile = "/Shared/paulsen/Experiments/rsFMRI/rs-fMRI-pilot/ReferenceAtlas/template_t1.nii.gz"
nacAtlasLabel = "/Shared/paulsen/Experiments/rsFMRI/rs-fMRI-pilot/ReferenceAtlas/template_nac_labels.nii.gz"
nacResampleResolution = (2.0, 2.0, 2.0)
downsampledNACfilename = 'downsampledNACatlas.nii.gz'
preproc = pipe.Workflow(name=CACHE_DIR)
preproc.base_dir = os.getcwd()
labels, seeds = getAtlasPoints(
'/Shared/paulsen/Experiments/rsFMRI/rs-fMRI-pilot/seeds.fcsv')
seedsIdentity = pipe.Node(interface=IdentityInterface(fields=['index']),
name='seedsIdentity')
seedsIdentity.iterables = ('index', range(len(labels)))
selectSeed = pipe.Node(interface=Select(), name='selectSeed')
selectSeed.inputs.inlist = seeds
preproc.connect(seedsIdentity, 'index', selectSeed, 'index')
selectLabel = pipe.Node(interface=Select(), name='selectLabel')
selectLabel.inputs.inlist = labels
preproc.connect(seedsIdentity, 'index', selectLabel, 'index')
points = pipe.Node(interface=Function(
function=createSphereExpression,
input_names=['coordinates', 'radius'],
output_names=['expression']),
name='createSphereExpression')
preproc.connect(selectSeed, 'out', points, 'coordinates')
downsampleAtlas = pipe.Node(interface=Function(
function=resampleImage,
input_names=['inputVolume', 'outputVolume', 'resolution'],
output_names=['outputVolume']),
name="downsampleAtlas")
downsampleAtlas.inputs.inputVolume = nacAtlasFile
downsampleAtlas.inputs.outputVolume = downsampledNACfilename
downsampleAtlas.inputs.resolution = [int(x) for x in nacResampleResolution]
spheres = pipe.Node(interface=Calc(letters=['a']), name='afni3Dcalc_seeds')
spheres.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(downsampleAtlas, 'outputVolume', spheres, 'in_file_a')
spheres.inputs.args = '-nscale'
preproc.connect(points, 'expression', spheres, 'expr')
renameMasks = pipe.Node(interface=Rename(format_string='%(label)s_mask'),
name='renameMasksAtlas')
renameMasks.inputs.keep_ext = True
preproc.connect(selectLabel, 'out', renameMasks, 'label')
preproc.connect(spheres, 'out_file', renameMasks, 'in_file')
atlas_DataSink = pipe.Node(interface=DataSink(), name="atlas_DataSink")
atlas_DataSink.inputs.base_directory = preproc.base_dir # '/Shared/paulsen/Experiments/20130417_rsfMRI_Results'
atlas_DataSink.inputs.container = RESULTS_DIR
atlas_DataSink.inputs.parameterization = False
atlas_DataSink.overwrite = REWRITE_DATASINKS
preproc.connect(renameMasks, 'out_file', atlas_DataSink, 'Atlas')
preproc.connect(downsampleAtlas, 'outputVolume', atlas_DataSink,
'Atlas.@resampled')
preproc.run()
def create_extended_susan_workflow(name='extended_susan', separate_masks=True):
input_node = pe.Node(IdentityInterface(fields=['in_file',
'fwhm',
'EPI_session_space',
'output_directory',
'sub_id']), name='inputspec')
output_node = pe.Node(interface=IdentityInterface(fields=['smoothed_files',
'mask',
'mean']), name='outputspec')
datasink = pe.Node(DataSink(), name='sinker')
datasink.inputs.parameterization = False
# first link the workflow's output_directory into the datasink.
esw = pe.Workflow(name=name)
esw.connect(input_node, 'output_directory', datasink, 'base_directory')
esw.connect(input_node, 'sub_id', datasink, 'container')
meanfuncmask = pe.Node(interface=fsl.BET(mask=True,
no_output=True,
frac=0.3),
name='meanfuncmask')
esw.connect(input_node, 'EPI_session_space', meanfuncmask, 'in_file')
"""
Mask the functional runs with the extracted mask
"""
maskfunc = pe.MapNode(interface=fsl.ImageMaths(suffix='_bet',
op_string='-mas'),
iterfield=['in_file'],
name='maskfunc')
esw.connect(input_node, 'in_file', maskfunc, 'in_file')
esw.connect(meanfuncmask, 'mask_file', maskfunc, 'in_file2')
"""
Determine the 2nd and 98th percentile intensities of each functional run
"""
getthresh = pe.MapNode(interface=fsl.ImageStats(op_string='-p 2 -p 98'),
iterfield=['in_file'],
name='getthreshold')
esw.connect(maskfunc, 'out_file', getthresh, 'in_file')
"""
Threshold the first run of the functional data at 10% of the 98th percentile
"""
threshold = pe.MapNode(interface=fsl.ImageMaths(out_data_type='char',
suffix='_thresh'),
iterfield=['in_file', 'op_string'],
name='threshold')
esw.connect(maskfunc, 'out_file', threshold, 'in_file')
"""
Define a function to get 10% of the intensity
"""
esw.connect(getthresh, ('out_stat', getthreshop), threshold, 'op_string')
"""
Determine the median value of the functional runs using the mask
"""
medianval = pe.MapNode(interface=fsl.ImageStats(op_string='-k %s -p 50'),
iterfield=['in_file', 'mask_file'],
name='medianval')
esw.connect(input_node, 'in_file', medianval, 'in_file')
esw.connect(threshold, 'out_file', medianval, 'mask_file')
"""
Dilate the mask
"""
dilatemask = pe.MapNode(interface=fsl.ImageMaths(suffix='_dil',
op_string='-dilF'),
iterfield=['in_file'],
name='dilatemask')
esw.connect(threshold, 'out_file', dilatemask, 'in_file')
esw.connect(dilatemask, 'out_file', output_node, 'mask')
"""
Mask the motion corrected functional runs with the dilated mask
"""
maskfunc2 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc2')
esw.connect(input_node, 'in_file', maskfunc2, 'in_file')
esw.connect(dilatemask, 'out_file', maskfunc2, 'in_file2')
"""
Smooth each run using SUSAN with the brightness threshold set to 75%
of the median value for each run and a mask constituting the mean
functional
"""
smooth = create_susan_smooth(separate_masks=separate_masks)
esw.connect(input_node, 'fwhm', smooth, 'inputnode.fwhm')
esw.connect(maskfunc2, 'out_file', smooth, 'inputnode.in_files')
esw.connect(dilatemask, 'out_file', smooth, 'inputnode.mask_file')
"""
Mask the smoothed data with the dilated mask
"""
maskfunc3 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc3')
esw.connect(smooth, 'outputnode.smoothed_files', maskfunc3, 'in_file')
esw.connect(dilatemask, 'out_file', maskfunc3, 'in_file2')
concatnode = pe.Node(interface=Merge(2),
name='concat')
esw.connect(maskfunc2, ('out_file', tolist), concatnode, 'in1')
esw.connect(maskfunc3, ('out_file', tolist), concatnode, 'in2')
"""
The following nodes select smooth or unsmoothed data depending on the
fwhm. This is because SUSAN defaults to smoothing the data with about the
voxel size of the input data if the fwhm parameter is less than 1/3 of the
voxel size.
"""
selectnode = pe.Node(interface=Select(), name='select')
esw.connect(concatnode, 'out', selectnode, 'inlist')
esw.connect(input_node, ('fwhm', chooseindex), selectnode, 'index')
esw.connect(selectnode, 'out', output_node, 'smoothed_files')
"""
Scale the median value of the run is set to 10000
"""
meanscale = pe.MapNode(interface=fsl.ImageMaths(suffix='_gms'),
iterfield=['in_file', 'op_string'],
name='meanscale')
esw.connect(selectnode, 'out', meanscale, 'in_file')
"""
Define a function to get the scaling factor for intensity normalization
"""
esw.connect(medianval, ('out_stat', getmeanscale), meanscale, 'op_string')
"""
Generate a mean functional image from the first run
"""
meanfunc3 = pe.Node(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='meanfunc3')
esw.connect(meanscale, ('out_file', pickfirst), meanfunc3, 'in_file')
esw.connect(meanfunc3, 'out_file', output_node, 'mean')
# Datasink
esw.connect(meanscale, 'out_file', datasink, 'filtering')
esw.connect(selectnode, 'out', datasink, 'filtering.@smoothed')
esw.connect(dilatemask, 'out_file', datasink, 'filtering.@mask')
return esw
==============================
"""
grab_anat = Node(BIDSDataGrabber(), name = 'grab_anat')
grab_anat.inputs.base_dir = os.path.join(project_dir, data_dir)
# Iterate through subjects; [:2] for only 2 subjects to keep memory usage low
grab_anat.iterables = ('subject', subject_list)
# Define filetypes to grab, and how ouput will be accesses by other nodes
grab_anat.inputs.output_query = {'T1w': dict(extension=['nii.gz'], suffix='T1w')}
#res = grab_anat.run()
# The Select utility interface
from nipype.interfaces.utility import Select
sel1 = Node(Select(), name='select1')
sel1.inputs.index = 0
wf.connect(grab_anat, 'T1w', sel1, 'inlist')
wf.run()
"""
============================================
Input of Functional Images
============================================
"""
grab_func = Node(BIDSDataGrabber(), name='grab_func')
grab_func.inputs.base_dir = os.path.join(project_dir, data_dir)
grab_func.inputs.output_query = {'bold': dict(extension=['nii.gz'], suffix='bold')}
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.field_template = dict(ct='%s/CT.nii.gz',
rtstruct='%s/RTSTRUCT/*.dcm')
datasource.inputs.template_args = dict(ct=[['sub_id']],
rtstruct=[['sub_id']])
datasource.inputs.raise_on_empty = False
datasource.inputs.sub_id = sub_list
voxelizer = nipype.MapNode(interface=Voxelizer(), iterfield=['reference', 'struct_file'],
name='voxelizer')
voxelizer.inputs.regular_expression = '.*PTV.*'
voxelizer.inputs.multi_structs = True
voxelizer.inputs.binarization = True
select = nipype.MapNode(interface=Select(), iterfield=['inlist'], name='select')
select.inputs.index = 0
features = nipype.MapNode(interface=CLGlobalFeatures(), iterfield=['in_file', 'mask'],
name='features_extraction')
features.inputs.first_order = True
features.inputs.cooccurence = True
features.inputs.run_length = True
features.inputs.int_vol_hist = True
features.inputs.local_intensity = True
features.inputs.volume = True
features.inputs.id = True
# features.inputs.ngld = True
features.inputs.ngtd = True
features.inputs.use_header = True
FslRoi.inputs.t_size = 1
#-----------------------------------------------------------------------------------------------------
# In[11]:
# mcflirt -in ${folder} -out ${folder}_mcf -refvol example_func -plots -mats -report;
McFlirt = Node(fsl.MCFLIRT(), name = 'McFlirt')
McFlirt.inputs.save_plots = True
McFlirt.inputs.save_mats = True
McFlirt.inputs.save_rms = True
McFlirt.inputs.output_type = 'NIFTI'
#-----------------------------------------------------------------------------------------------------
#Getting motion parameters from Mcflirt and plotting them
Get_Abs_Displacement = Node(Select(), name = 'Get_Absolute_Displacement')
Get_Abs_Displacement.inputs.index = [0]
Get_Rel_Displacement = Node(Select(), name = 'Get_Relative_Displacement')
Get_Rel_Displacement.inputs.index = [1]
def Plot_Motion(motion_par, abs_disp, rel_disp):
import numpy as np
import matplotlib.pyplot as plt
movement = np.loadtxt(motion_par)
abs_disp = np.loadtxt(abs_disp)
rel_disp = np.loadtxt(rel_disp)
def spm_anat_to_diff_coregistration(wf_name="spm_anat_to_diff_coregistration"):
""" Co-register the anatomical image and other images in anatomical space to
the average B0 image.
This estimates an affine transform from anat to diff space, applies it to
the brain mask and an atlas.
Nipype Inputs
-------------
dti_co_input.avg_b0: traits.File
path to the average B0 image from the diffusion MRI.
This image should come from a motion and Eddy currents
corrected diffusion image.
dti_co_input.anat: traits.File
path to the high-contrast anatomical image.
dti_co_input.tissues: traits.File
paths to the NewSegment c*.nii output files, in anatomical space
dti_co_input.atlas_anat: traits.File
Atlas in subject anatomical space.
Nipype Outputs
--------------
dti_co_output.anat_diff: traits.File
Anatomical image in diffusion space.
dti_co_output.tissues_diff: traits.File
Tissues images in diffusion space.
dti_co_output.brain_mask_diff: traits.File
Brain mask for diffusion image.
dti_co_output.atlas_diff: traits.File
Atlas image warped to diffusion space.
If the `atlas_file` option is an existing file and `normalize_atlas` is True.
Nipype Workflow Dependencies
----------------------------
This workflow depends on:
- spm_anat_preproc
Returns
-------
wf: nipype Workflow
"""
# specify input and output fields
in_fields = ["avg_b0", "tissues", "anat"]
out_fields = [
"anat_diff",
"tissues_diff",
"brain_mask_diff",
]
do_atlas, _ = check_atlas_file()
if do_atlas:
in_fields += ["atlas_anat"]
out_fields += ["atlas_diff"]
# input interface
dti_input = pe.Node(IdentityInterface(fields=in_fields,
mandatory_inputs=True),
name="dti_co_input")
gunzip_b0 = pe.Node(Gunzip(), name="gunzip_b0")
coreg_b0 = setup_node(spm_coregister(cost_function="mi"), name="coreg_b0")
# co-registration
brain_sel = pe.Node(Select(index=[0, 1, 2]), name="brain_sel")
coreg_split = pe.Node(Split(splits=[1, 2], squeeze=True),
name="coreg_split")
brain_merge = setup_node(MultiImageMaths(), name="brain_merge")
brain_merge.inputs.op_string = "-add '%s' -add '%s' -abs -kernel gauss 4 -dilM -ero -kernel gauss 1 -dilM -bin"
brain_merge.inputs.out_file = "brain_mask_diff.nii.gz"
# output interface
dti_output = pe.Node(IdentityInterface(fields=out_fields),
name="dti_co_output")
# Create the workflow object
wf = pe.Workflow(name=wf_name)
# Connect the nodes
wf.connect([
# co-registration
(dti_input, coreg_b0, [("anat", "source")]),
(dti_input, brain_sel, [("tissues", "inlist")]),
(brain_sel, coreg_b0, [(("out", flatten_list), "apply_to_files")]),
(dti_input, gunzip_b0, [("avg_b0", "in_file")]),
(gunzip_b0, coreg_b0, [("out_file", "target")]),
(coreg_b0, coreg_split, [("coregistered_files", "inlist")]),
(coreg_split, brain_merge, [("out1", "in_file")]),
(coreg_split, brain_merge, [("out2", "operand_files")]),
# output
(coreg_b0, dti_output, [("coregistered_source", "anat_diff")]),
(coreg_b0, dti_output, [("coregistered_files", "tissues_diff")]),
(brain_merge, dti_output, [("out_file", "brain_mask_diff")]),
])
# add more nodes if to perform atlas registration
if do_atlas:
coreg_atlas = setup_node(spm_coregister(cost_function="mi"),
name="coreg_atlas")
# set the registration interpolation to nearest neighbour.
coreg_atlas.inputs.write_interp = 0
wf.connect([
(dti_input, coreg_atlas, [
("anat", "source"),
("atlas_anat", "apply_to_files"),
]),
(gunzip_b0, coreg_atlas, [("out_file", "target")]),
(coreg_atlas, dti_output, [("coregistered_files", "atlas_diff")]),
])
return wf