def test_normalize_list_outputs():
filelist, outdir, cwd = create_files_in_directory()
norm = spm.Normalize(source=filelist[0])
yield assert_true, norm._list_outputs()['normalized_source'][0].startswith(
'w')
norm = spm.Normalize(source=filelist[0], apply_to_files=filelist[1])
yield assert_true, norm._list_outputs()['normalized_files'][0].startswith(
'w')
clean_directory(outdir, cwd)
def __init__(self, experiment_dir, output_dir, working_dir, func_source,
struct_source, datasink):
self.experiment_dir = experiment_dir
self.output_dir = output_dir
self.working_dir = working_dir
# specify input and output nodes
self.func_source = func_source
self.struct_source = struct_source
self.datasink = datasink
# specify workflow instance
self.workflow = pe.Workflow(name='workflow')
# specify nodes
self.realign = pe.Node(interface=spm.Realign(), name='realign')
self.coregister = pe.Node(interface=spm.Coregister(),
name="coregister")
self.coregister.inputs.jobtype = 'estimate'
self.segment = pe.Node(interface=spm.Segment(), name="segment")
self.normalize_func = pe.Node(interface=spm.Normalize(),
name="normalize_func")
self.normalize_func.inputs.jobtype = "write"
self.normalize_struc = pe.Node(interface=spm.Normalize(),
name="normalize_struc")
self.normalize_struc.inputs.jobtype = "write"
self.smooth = pe.Node(interface=spm.Smooth(), name="smooth")
# connect the nodes to complete the workflow
self.workflow.connect([
(self.func_source, self.realign, [('outfiles', 'in_files')]),
(self.struct_source, self.coregister, [('outfiles', 'source')]),
(self.realign, self.coregister, [('mean_image', 'target')]),
(self.coregister, self.segment, [('coregistered_source', 'data')]),
(self.segment, self.normalize_func, [('transformation_mat',
'parameter_file')]),
(self.realign, self.normalize_func, [('realigned_files',
'apply_to_files')]),
(self.normalize_func, self.smooth, [('normalized_files',
'in_files')]),
#(self.realign, self.datasink, [('realigned_files', 'realign')]),
#(self.realign, self.datasink, [('mean_image', 'mean')]),
(self.normalize_func, self.datasink, [('normalized_files', 'norm')]
),
(self.smooth, self.datasink, [('smoothed_files', 'smooth')])
])
def __init__(self,
parameter_file='path',
source=['path'],
template='path',
**options):
import nipype.interfaces.spm as spm
norm = spm.Normalize()
norm.inputs.parameter_file = parameter_file
norm.inputs.source = source
norm.inputs.template = template
for ef in options:
setattr(norm.inputs, ef, options[ef])
self.res = norm.run()
def test_normalize():
yield assert_equal, spm.Normalize._jobtype, 'spatial'
yield assert_equal, spm.Normalize._jobname, 'normalise'
yield assert_equal, spm.Normalize().inputs.jobtype, 'estwrite'
input_map = dict(template=dict(field='eoptions.template',
mandatory=True,
xor=['parameter_file'],
copyfile=False),
source=dict(field='subj.source',
xor=['parameter_file'],
mandatory=True,
copyfile=True),
apply_to_files=dict(field='subj.resample', copyfile=True),
parameter_file=dict(field='subj.matname',
mandatory=True,
xor=['source', 'template'],
copyfile=False),
source_weight=dict(field='subj.wtsrc', copyfile=False),
template_weight=dict(field='eoptions.weight',
copyfile=False),
source_image_smoothing=dict(field='eoptions.smosrc'),
template_image_smoothing=dict(field='eoptions.smoref'),
affine_regularization_type=dict(field='eoptions.regype'),
DCT_period_cutoff=dict(field='eoptions.cutoff'),
nonlinear_iterations=dict(field='eoptions.nits'),
nonlinear_regularization=dict(field='eoptions.reg'),
write_preserve=dict(field='roptions.preserve'),
write_bounding_box=dict(field='roptions.bb'),
write_voxel_sizes=dict(field='roptions.vox'),
write_interp=dict(field='roptions.interp'),
write_wrap=dict(field='roptions.wrap'))
norm = spm.Normalize()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(norm.inputs.traits()[key],
metakey), value
def simple_warp(template, warped, other=None):
""" uses basic spm Normalize to warp warped to template
applies parameters to other if specified"""
startdir = os.getcwd()
pth, _ = os.path.split(warped)
os.chdir(pth)
warp = spm.Normalize(matlab_cmd='matlab-spm8')
warp.inputs.template = template
warp.inputs.source = warped
warp.inputs.ignore_exception = True
if other is not None:
warp.inputs.apply_to_files = other
warp_out = warp.run()
os.chdir(startdir)
return warp_out
def normalize_T1_toMNI152(T1_dir, slice_time_dir):
# Function normalizes an AC-PC aligned T1 into MNI 152 space
# Get the name of the ac-pc aligned T1
os.chdir(T1_dir)
for files in os.listdir(T1_dir):
if files.startswith('r'):
T1name = files
# Get list of EPIs to apply MNI normalization transform result from T1
EPI_list = []
os.chdir(slice_time_dir)
for files in os.listdir(slice_time_dir):
if files.startswith('ar'):
EPI_list.append(files)
# Initialize SPM normalization
EPI_list.sort()
mni_template = matlab_dir + '/toolbox/spm8/canonical/avg152T1.nii'
os.system('cp %s %s' % (mni_template, slice_time_dir))
# copy spm mni template to cwd
norm = spm.Normalize()
norm.inputs.source = T1_dir + '/' + T1name
norm.inputs.template = mni_template
norm.inputs.affine_regularization_type = 'mni'
EPI_list.append(norm.inputs.source)
# apply normalization to T1 and all EPIs
norm.inputs.apply_to_files = EPI_list
print "<:::Normalizing T1 and EPIs to MNI 152:::>"
norm.run()
# Make a new dir for MNI warped EPIs
MNI_dir = os.mkdir('MNI_Normalized')
os.system('cp w* %s' % (MNI_dir))
return MNI_dir
"""
skullstrip = pe.Node(fsl.BET(), name="skullstrip")
skullstrip.inputs.mask = True
"""Use :class:`nipype.interfaces.spm.Coregister` to perform a rigid
body registration of the functional data to the structural data.
"""
coregister = pe.Node(spm.Coregister(), name="coregister")
coregister.inputs.jobtype = 'estimate'
"""Warp functional and structural data to SPM's T1 template using
:class:`nipype.interfaces.spm.Normalize`. The tutorial data set
includes the template image, T1.nii.
"""
normalize = pe.Node(spm.Normalize(), name="normalize")
"""Smooth the functional data using
:class:`nipype.interfaces.spm.Smooth`.
"""
smooth = pe.Node(spm.Smooth(), name="smooth")
fwhmlist = [4]
smooth.iterables = ('fwhm', fwhmlist)
preproc.connect([
(inputnode, normalize, [(('in_data', _template_path), 'template')]),
(realign, coregister, [('mean_image', 'source'),
('realigned_files', 'apply_to_files')]),
(coregister, normalize, [('coregistered_files', 'apply_to_files')]),
(normalize, smooth, [('normalized_files', 'in_files')]),
(normalize, skullstrip, [('normalized_source', 'in_file')]),
"""
skullstrip = pe.Node(interface=fsl.BET(), name="skullstrip")
skullstrip.inputs.mask = True
"""Use :class:`nipype.interfaces.spm.Coregister` to perform a rigid
body registration of the functional data to the structural data.
"""
coregister = pe.Node(interface=spm.Coregister(), name="coregister")
coregister.inputs.jobtype = 'estimate'
"""Warp functional and structural data to SPM's T1 template using
:class:`nipype.interfaces.spm.Normalize`. The tutorial data set
includes the template image, T1.nii.
"""
normalize = pe.Node(interface=spm.Normalize(), name="normalize")
normalize.inputs.template = os.path.abspath('data/T1.nii')
"""Smooth the functional data using
:class:`nipype.interfaces.spm.Smooth`.
"""
smooth = pe.Node(interface=spm.Smooth(), name="smooth")
fwhmlist = [4]
smooth.iterables = ('fwhm', fwhmlist)
preproc.connect([
(realign, coregister, [('mean_image', 'source'),
('realigned_files', 'apply_to_files')]),
(coregister, normalize, [('coregistered_files', 'apply_to_files')]),
(normalize, smooth, [('normalized_files', 'in_files')]),
(normalize, skullstrip, [('normalized_source', 'in_file')]),
segment = pe.Node(interface=spm.Segment(), name='segment')
"""
Use :class:`nipype.interfaces.freesurfer.ApplyVolTransform` to convert contrast
images into freesurfer space.
"""
normwreg = pe.MapNode(interface=fs.ApplyVolTransform(),
iterfield=['source_file'],
name='applyreg2con')
"""
Use :class:`nipype.interfaces.spm.Normalize` to normalize the contrast images
to MNI space
"""
normalize = pe.Node(interface=spm.Normalize(jobtype='write'), name='norm2mni')
"""
Connect up the volume normalization components
"""
volnorm.connect([
(convert, segment, [('out_file', 'data')]),
(convert2, normwreg, [('out_file', 'source_file')]),
(segment, normalize, [('transformation_mat', 'parameter_file')]),
(normwreg, normalize, [('transformed_file', 'apply_to_files')]),
])
"""
Preproc + Analysis + VolumeNormalization workflow
-------------------------------------------------
Connect up the lower level workflows into an integrated analysis. In addition,
def test_normalize_list_outputs(create_files_in_directory):
filelist, outdir, cwd = create_files_in_directory
norm = spm.Normalize(source=filelist[0])
assert norm._list_outputs()['normalized_source'][0].startswith('w')
norm = spm.Normalize(source=filelist[0], apply_to_files=filelist[1])
assert norm._list_outputs()['normalized_files'][0].startswith('w')
def test_normalize():
assert spm.Normalize._jobtype == 'spatial'
assert spm.Normalize._jobname == 'normalise'
assert spm.Normalize().inputs.jobtype == 'estwrite'
def create_spm_preproc_func_pipeline(data_dir=None,
subject_id=None,
task_list=None):
###############################
## Set up Nodes
###############################
ds = Node(nio.DataGrabber(infields=['subject_id', 'task_id'],
outfields=['func', 'struc']),
name='datasource')
ds.inputs.base_directory = os.path.abspath(data_dir + '/' + subject_id)
ds.inputs.template = '*'
ds.inputs.sort_filelist = True
ds.inputs.template_args = {'func': [['task_id']], 'struc': []}
ds.inputs.field_template = {
'func': 'Functional/Raw/%s/func.nii',
'struc': 'Structural/SPGR/spgr.nii'
}
ds.inputs.subject_id = subject_id
ds.inputs.task_id = task_list
ds.iterables = ('task_id', task_list)
# ds.run().outputs #show datafiles
# #Setup Data Sinker for writing output files
# datasink = Node(nio.DataSink(), name='sinker')
# datasink.inputs.base_directory = '/path/to/output'
# workflow.connect(realigner, 'realignment_parameters', datasink, 'motion.@par')
# datasink.inputs.substitutions = [('_variable', 'variable'),('file_subject_', '')]
#Get Timing Acquisition for slice timing
tr = 2
ta = Node(interface=util.Function(input_names=['tr', 'n_slices'],
output_names=['ta'],
function=get_ta),
name="ta")
ta.inputs.tr = tr
#Slice Timing: sequential ascending
slice_timing = Node(interface=spm.SliceTiming(), name="slice_timing")
slice_timing.inputs.time_repetition = tr
slice_timing.inputs.ref_slice = 1
#Realignment - 6 parameters - realign to first image of very first series.
realign = Node(interface=spm.Realign(), name="realign")
realign.inputs.register_to_mean = True
#Plot Realignment
plot_realign = Node(interface=PlotRealignmentParameters(),
name="plot_realign")
#Artifact Detection
art = Node(interface=ra.ArtifactDetect(), name="art")
art.inputs.use_differences = [True, False]
art.inputs.use_norm = True
art.inputs.norm_threshold = 1
art.inputs.zintensity_threshold = 3
art.inputs.mask_type = 'file'
art.inputs.parameter_source = 'SPM'
#Coregister - 12 parameters, cost function = 'nmi', fwhm 7, interpolate, don't mask
#anatomical to functional mean across all available data.
coregister = Node(interface=spm.Coregister(), name="coregister")
coregister.inputs.jobtype = 'estimate'
# Segment structural, gray/white/csf,mni,
segment = Node(interface=spm.Segment(), name="segment")
segment.inputs.save_bias_corrected = True
#Normalize - structural to MNI - then apply this to the coregistered functionals
normalize = Node(interface=spm.Normalize(), name="normalize")
normalize.inputs.template = os.path.abspath(t1_template_file)
#Plot normalization Check
plot_normalization_check = Node(interface=Plot_Coregistration_Montage(),
name="plot_normalization_check")
plot_normalization_check.inputs.canonical_img = canonical_file
#Create Mask
compute_mask = Node(interface=ComputeMask(), name="compute_mask")
#remove lower 5% of histogram of mean image
compute_mask.inputs.m = .05
#Smooth
#implicit masking (.im) = 0, dtype = 0
smooth = Node(interface=spm.Smooth(), name="smooth")
fwhmlist = [0, 5, 8]
smooth.iterables = ('fwhm', fwhmlist)
#Create Covariate matrix
make_covariates = Node(interface=Create_Covariates(),
name="make_covariates")
###############################
## Create Pipeline
###############################
Preprocessed = Workflow(name="Preprocessed")
Preprocessed.base_dir = os.path.abspath(data_dir + '/' + subject_id +
'/Functional')
Preprocessed.connect([
(ds, ta, [(('func', get_n_slices), "n_slices")]),
(ta, slice_timing, [("ta", "time_acquisition")]),
(ds, slice_timing, [
('func', 'in_files'),
(('func', get_n_slices), "num_slices"),
(('func', get_slice_order), "slice_order"),
]),
(slice_timing, realign, [('timecorrected_files', 'in_files')]),
(realign, compute_mask, [('mean_image', 'mean_volume')]),
(realign, coregister, [('mean_image', 'target')]),
(ds, coregister, [('struc', 'source')]),
(coregister, segment, [('coregistered_source', 'data')]),
(segment, normalize, [
('transformation_mat', 'parameter_file'),
('bias_corrected_image', 'source'),
]),
(realign, normalize, [('realigned_files', 'apply_to_files'),
(('realigned_files', get_vox_dims),
'write_voxel_sizes')]),
(normalize, smooth, [('normalized_files', 'in_files')]),
(compute_mask, art, [('brain_mask', 'mask_file')]),
(realign, art, [('realignment_parameters', 'realignment_parameters')]),
(realign, art, [('realigned_files', 'realigned_files')]),
(realign, plot_realign, [('realignment_parameters',
'realignment_parameters')]),
(normalize, plot_normalization_check, [('normalized_files', 'wra_img')
]),
(realign, make_covariates, [('realignment_parameters',
'realignment_parameters')]),
(art, make_covariates, [('outlier_files', 'spike_id')]),
])
return Preprocessed
def __init__(self,
subject,
func_source,
struct_source,
datasink,
TR,
num_slices,
dim=2):
self.subject = subject
# specify input and output nodes
self.func_source = func_source
self.struct_source = struct_source
self.datasink = datasink
self.TR = TR
self.num_slices = num_slices
# specify nodes
# structual process
self.bet_struct = pe.Node(interface=fsl.BET(),
name='non_brain_removal_BET_struct')
self.bet_struct.inputs.output_type = "NIFTI"
self.bet_struct.inputs.frac = 0.3
self.coregister_struct = pe.Node(interface=spm.Coregister(),
name="coregister_struct_to_mni")
self.coregister_struct.inputs.target = '/mnt/Program/python/dev/images/MNI152_T1_2mm_brain.nii'
if dim == 1:
self.coregister_struct.inputs.target = '/mnt/Program/python/dev/images/MNI152_T1_1mm_brain.nii'
self.coregister_struct.inputs.write_interp = 7
self.coregister_struct.inputs.separation = [1.0, 1.0]
self.coregister_struct.inputs.jobtype = 'estwrite'
self.segment_struct = pe.Node(interface=spm.Segment(),
name="segment_struct")
# self.segment_struct.inputs.affine_regularization = 'mni'
self.segment_struct.inputs.csf_output_type = [True, True, True]
self.segment_struct.inputs.gm_output_type = [True, True, True]
self.segment_struct.inputs.wm_output_type = [True, True, True]
self.normalize_struct = pe.Node(interface=spm.Normalize(),
name='normalize_struct')
self.normalize_struct.inputs.jobtype = 'write'
self.normalize_struct.inputs.write_bounding_box = [[-90, -126, -72],
[90, 90, 108]
] # 91, 109, 91
if dim == 1:
self.normalize_struct.inputs.write_bounding_box = [[
-91, -126, -72
], [90, 91, 109]] # 182, 218, 182
self.normalize_struct.inputs.write_voxel_sizes = [1, 1, 1]
self.normalize_gm = pe.Node(interface=spm.Normalize(),
name='normalize_gm')
self.normalize_gm.inputs.jobtype = 'write'
self.normalize_gm.inputs.write_bounding_box = [[-90, -126, -72],
[90, 90,
108]] # 91, 109, 91
if dim == 1:
self.normalize_gm.inputs.write_bounding_box = [[-91, -126, -72],
[90, 91, 109]
] # 182, 218, 182
self.normalize_gm.inputs.write_voxel_sizes = [1, 1, 1]
self.normalize_wm = pe.Node(interface=spm.Normalize(),
name='normalize_wm')
self.normalize_wm.inputs.jobtype = 'write'
self.normalize_wm.inputs.write_bounding_box = [[-90, -126, -72],
[90, 90,
108]] # 91, 109, 91
if dim == 1:
self.normalize_wm.inputs.write_bounding_box = [[-91, -126, -72],
[90, 91, 109]
] # 182, 218, 182
self.normalize_wm.inputs.write_voxel_sizes = [1, 1, 1]
self.normalize_csf = pe.Node(interface=spm.Normalize(),
name='normalize_csf')
self.normalize_csf.inputs.jobtype = 'write'
self.normalize_csf.inputs.write_bounding_box = [[-90, -126, -72],
[90, 90,
108]] # 91, 109, 91
if dim == 1:
self.normalize_csf.inputs.write_bounding_box = [[-91, -126, -72],
[90, 91, 109]
] # 182, 218, 182
self.normalize_csf.inputs.write_voxel_sizes = [1, 1, 1]
###################################################################################################
# functional process
self.fslsplit = pe.Node(interface=fsl.Split(), name='fslsplit')
self.fslsplit.inputs.dimension = 't'
self.fslsplit.inputs.output_type = "NIFTI"
self.fslmerge = pe.Node(interface=fsl.Merge(), name='fslmerge')
self.fslmerge.inputs.dimension = 't'
self.fslmerge.inputs.output_type = "NIFTI"
# helper function(s)
def bet_each(in_files, subject_name):
'''
@param in_files: list of image files
@return out_files: list of image files after applied fsl.BET on it
'''
from nipype.interfaces import fsl
import nipype.pipeline.engine as pe
out_files = list()
step_no = 0
for file_ in in_files:
bet = pe.Node(interface=fsl.BET(),
name='BET_for_step_{}_{}'.format(
step_no, subject_name))
bet.inputs.in_file = file_
bet.inputs.out_file = file_[:len(file_) - 4] + '_bet.nii'
bet.inputs.output_type = "NIFTI"
bet.inputs.frac = 0.5
bet.run()
out_files.append(bet.inputs.out_file)
step_no += 1
return out_files
# bet_func return a list of NIFITI files
self.bet_func = pe.Node(interface=Function(
input_names=['in_files', 'subject_name'],
output_names=['out_files'],
function=bet_each),
name='non_brain_removal_BET_func')
self.bet_func.inputs.subject_name = self.subject
self.realign = pe.Node(interface=spm.Realign(),
name='realign_motion_correction')
self.realign.inputs.register_to_mean = True
self.coregister_func = pe.Node(interface=spm.Coregister(),
name="coregister_func_to_mni")
self.coregister_func.inputs.target = '/mnt/Program/python/dev/images/MNI152_T1_2mm_brain.nii'
self.coregister_func.inputs.write_interp = 7
self.coregister_func.inputs.separation = [1.0, 1.0]
self.coregister_func.inputs.jobtype = 'estwrite'
self.segment = pe.Node(interface=spm.Segment(), name="segment")
self.normalize_func = pe.Node(interface=spm.Normalize(),
name="normalize_func")
self.normalize_func.inputs.jobtype = 'write'
self.normalize_func.inputs.write_bounding_box = [[-90, -126, -72],
[90, 90,
108]] # 91, 109, 91
self.smooth = pe.Node(interface=spm.Smooth(), name="smooth")
self.smooth.inputs.fwhm = [8, 8, 8]
# backup node(s)
self.slice_timing = pe.Node(interface=spm.SliceTiming(),
name='time_slice_correction')
self.slice_timing.inputs.time_repetition = self.TR
self.slice_timing.inputs.num_slices = self.num_slices
self.slice_timing.inputs.time_acquisition = self.TR - (self.TR /
self.num_slices)
self.slice_timing.inputs.slice_order = list(
range(self.num_slices, 0, -1))
self.slice_timing.inputs.ref_slice = 1
self.direct_normalize = pe.Node(interface=spm.Normalize12(),
name='direct_normalize')
self.direct_normalize.inputs.image_to_align = 'images/MNI152_T1_2mm_brain.nii'
self.direct_normalize.inputs.affine_regularization_type = 'size'
# specify workflow instance
self.workflow = pe.Workflow(name='preprocess_workflow')
# connect nodes
self.workflow.connect([
(self.struct_source, self.bet_struct, [('outfiles', 'in_file')]),
(self.bet_struct, self.coregister_struct, [('out_file', 'source')
]),
(self.coregister_struct, self.segment_struct,
[('coregistered_source', 'data')]),
(self.segment_struct, self.normalize_struct,
[('transformation_mat', 'parameter_file')]),
(self.coregister_struct, self.normalize_struct,
[('coregistered_source', 'apply_to_files')]),
(self.segment_struct, self.normalize_gm, [('transformation_mat',
'parameter_file')]),
(self.segment_struct, self.normalize_gm, [('native_gm_image',
'apply_to_files')]),
(self.segment_struct, self.normalize_wm, [('transformation_mat',
'parameter_file')]),
(self.segment_struct, self.normalize_wm, [('native_wm_image',
'apply_to_files')]),
(self.segment_struct, self.normalize_csf, [('transformation_mat',
'parameter_file')]),
(self.segment_struct, self.normalize_csf, [('native_csf_image',
'apply_to_files')]),
(self.func_source, self.fslsplit, [('outfiles', 'in_file')]),
(self.fslsplit, self.bet_func, [('out_files', 'in_files')]),
(self.bet_func, self.fslmerge, [('out_files', 'in_files')]),
(self.fslmerge, self.realign, [('merged_file', 'in_files')]),
(self.realign, self.datasink, [('realignment_parameters',
'realignment_parameters')]),
(self.realign, self.coregister_func, [('mean_image', 'source')]),
(self.realign, self.coregister_func, [('realigned_files',
'apply_to_files')]),
(self.coregister_func, self.segment, [('coregistered_source',
'data')]),
(self.segment, self.normalize_func, [('transformation_mat',
'parameter_file')]),
(self.coregister_func, self.normalize_func, [('coregistered_files',
'apply_to_files')]),
(self.normalize_func, self.smooth, [('normalized_files',
'in_files')]), # end
(self.normalize_func, self.datasink, [('normalized_files',
'before_smooth')]),
(self.smooth, self.datasink, [('smoothed_files', 'final_out')]),
(self.normalize_struct, self.datasink,
[('normalized_files', 'standardized_struct_file')]),
# (self.segment_struct, self.datasink, [('native_csf_image', 'csf'), ('native_gm_image', 'grey_matter'), ('native_wm_image', 'white_matter')])
(self.normalize_gm, self.datasink, [('normalized_files',
'grey_matter')]),
(self.normalize_wm, self.datasink, [('normalized_files',
'white_matter')]),
(self.normalize_csf, self.datasink, [('normalized_files', 'csf')]),
])
# backup workflow(s)
self.workflow_only_fmri = pe.Workflow(name='preprocess_workflow')
# connect nodes
self.workflow_only_fmri.connect([
(self.func_source, self.fslsplit, [('outfiles', 'in_file')]),
(self.fslsplit, self.bet_func, [('out_files', 'in_files')]),
(self.bet_func, self.fslmerge, [('out_files', 'in_files')]),
(self.fslmerge, self.realign, [('merged_file', 'in_files')]),
(self.realign, self.direct_normalize, [('realigned_files',
'apply_to_files')]),
(self.direct_normalize, self.smooth, [('normalized_files',
'in_files')]), # end
(self.direct_normalize, self.datasink, [('normalized_files',
'before_smooth')]),
(self.smooth, self.datasink, [('smoothed_files', 'final_out')])
])
def test_normalize():
assert spm.Normalize._jobtype == "spatial"
assert spm.Normalize._jobname == "normalise"
assert spm.Normalize().inputs.jobtype == "estwrite"
def spm_mrpet_grouptemplate_preprocessing(wf_name="spm_mrpet_grouptemplate_preproc"):
""" Run the PET pre-processing workflow against the gunzip_pet.in_file files.
It depends on the anat_preproc_workflow, so if this has not been run, this function
will run it too.
This is identical to the workflow defined in `spm_mrpet_preprocessing`,
with the only difference that we now normalize all subjects agains a custom
template using the spm Old Normalize interface.
It does:
- SPM12 Coregister T1 and tissues to PET
- PVC the PET image in PET space
- SPM12 Warp PET to the given template
Parameters
----------
wf_name: str
Name of the workflow.
Nipype Inputs
-------------
pet_input.in_file: traits.File
The raw NIFTI_GZ PET image file.
pet_input.atlas_anat: traits.File
The atlas file in anatomical space.
pet_input.anat: traits.File
Path to the high-contrast anatomical image.
Reference file of the warp_field, i.e., the anatomical image in its native space.
pet_input.tissues: list of traits.File
List of tissues files from the New Segment process. At least the first
3 tissues must be present.
pet_input.pet_template: traits.File
The template file for inter-subject registration reference.
Nipype outputs
--------------
pet_output.pvc_out: existing file
The results of the PVC process.
pet_output.brain_mask: existing file
A brain mask calculated with the tissues file.
pet_output.coreg_ref: existing file
The coregistered reference image to PET space.
pet_output.coreg_others: list of existing files
List of coregistered files from coreg_pet.apply_to_files.
pet_output.pet_warped: existing file
PET image normalized to the group template.
pet_output.pvc_warped: existing file
The outputs of the PETPVC workflow normalized to the group template.
The result of every internal pre-processing step is normalized to the
group template here.
pet_output.warp_field: existing files
Spatial normalization parameters .mat files.
pet_output.gm_norm: existing file
The output of the grey matter intensity normalization process.
This is the last step in the PET signal correction, before registration.
pet_output.atlas_pet: existing file
Atlas image warped to PET space.
If the `atlas_file` option is an existing file and `normalize_atlas` is True.
Returns
-------
wf: nipype Workflow
"""
# specify input and output fields
in_fields = ["in_file",
"anat",
"tissues",
"pet_template"]
out_fields = ["brain_mask",
"coreg_others",
"coreg_ref",
"pvc_warped",
"pet_warped",
"warp_field",
"pvc_out",
"pvc_mask",
"gm_norm",]
do_atlas, _ = check_atlas_file()
if do_atlas:
in_fields += ["atlas_anat"]
out_fields += ["atlas_pet" ]
# input
pet_input = setup_node(IdentityInterface(fields=in_fields, mandatory_inputs=True),
name="pet_input")
# workflow to perform partial volume correction
petpvc = petpvc_workflow(wf_name="petpvc")
unzip_mrg = setup_node(Merge(4), name='merge_for_unzip')
gunzipper = pe.MapNode(Gunzip(), name="gunzip", iterfield=['in_file'])
# warp each subject to the group template
gunzip_template = setup_node(Gunzip(), name="gunzip_template",)
gunzip_pet = setup_node(Gunzip(), name="gunzip_pet",)
warp_mrg = setup_node(Merge(2), name='merge_for_warp')
warp2template = setup_node(spm.Normalize(jobtype="estwrite", out_prefix="wgrptemplate_"),
name="warp2template",)
get_bbox = setup_node(Function(function=get_bounding_box,
input_names=["in_file"],
output_names=["bbox"]),
name="get_bbox")
# output
pet_output = setup_node(IdentityInterface(fields=out_fields), name="pet_output")
# Create the workflow object
wf = pe.Workflow(name=wf_name)
wf.connect([
# inputs
(pet_input, petpvc, [("in_file", "pvc_input.in_file"),
("anat", "pvc_input.reference_file"),
("tissues", "pvc_input.tissues")]),
# get template bounding box to apply to results
(pet_input, get_bbox, [("pet_template", "in_file")]),
# gunzip some inputs
(pet_input, gunzip_pet, [("in_file", "in_file")]),
(pet_input, gunzip_template, [("pet_template", "in_file")]),
# gunzip some files for SPM Normalize
(petpvc, unzip_mrg, [("pvc_output.pvc_out", "in1"),
("pvc_output.brain_mask", "in2"),
("pvc_output.gm_norm", "in3")]),
(pet_input, unzip_mrg, [("in_file", "in4")]),
(unzip_mrg, gunzipper, [("out", "in_file")]),
(gunzipper, warp_mrg, [("out_file", "in1")]),
(warp_mrg, warp2template, [(("out", flatten_list), "apply_to_files")]),
# prepare the target parameters of the warp to template
(gunzip_pet, warp2template, [("out_file", "source")]),
(gunzip_template, warp2template, [("out_file", "template")]),
(get_bbox, warp2template, [("bbox", "write_bounding_box")]),
# output
(warp2template, pet_output, [("normalization_parameters", "warp_field"),
("normalized_files" , "pvc_warped"),
("normalized_source", "pet_warped"),
]),
# output
(petpvc, pet_output, [("pvc_output.pvc_out", "pvc_out"),
("pvc_output.brain_mask", "brain_mask"),
("pvc_output.coreg_ref", "coreg_ref"),
("pvc_output.coreg_others", "coreg_others"),
("pvc_output.gm_norm", "gm_norm")]),
])
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([
(pet_input, coreg_atlas, [("anat", "source")]),
(petpvc, coreg_atlas, [("pvc_output.coreg_ref", "target")]),
(pet_input, coreg_atlas, [("atlas_anat", "apply_to_files")]),
(coreg_atlas, pet_output, [("coregistered_files", "atlas_pet")]),
# warp the atlas to the template space as well
(coreg_atlas, warp_mrg, [("coregistered_files", "in2")]),
])
return wf
def create_spm_preproc(c, name='preproc'):
"""Create an spm preprocessing workflow with freesurfer registration and
artifact detection.
The workflow realigns and smooths and registers the functional images with
the subject's freesurfer space.
Example
-------
>>> preproc = create_spm_preproc()
>>> preproc.base_dir = '.'
>>> preproc.inputs.inputspec.fwhm = 6
>>> preproc.inputs.inputspec.subject_id = 's1'
>>> preproc.inputs.inputspec.subjects_dir = '.'
>>> preproc.inputs.inputspec.functionals = ['f3.nii', 'f5.nii']
>>> preproc.inputs.inputspec.norm_threshold = 1
>>> preproc.inputs.inputspec.zintensity_threshold = 3
Inputs::
inputspec.functionals : functional runs use 4d nifti
inputspec.subject_id : freesurfer subject id
inputspec.subjects_dir : freesurfer subjects dir
inputspec.fwhm : smoothing fwhm
inputspec.norm_threshold : norm threshold for outliers
inputspec.zintensity_threshold : intensity threshold in z-score
Outputs::
outputspec.realignment_parameters : realignment parameter files
outputspec.smoothed_files : smoothed functional files
outputspec.outlier_files : list of outliers
outputspec.outlier_stats : statistics of outliers
outputspec.outlier_plots : images of outliers
outputspec.mask_file : binary mask file in reference image space
outputspec.reg_file : registration file that maps reference image to
freesurfer space
outputspec.reg_cost : cost of registration (useful for detecting misalignment)
"""
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
import nipype.algorithms.rapidart as ra
import nipype.interfaces.spm as spm
import nipype.interfaces.utility as niu
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
"""
Initialize the workflow
"""
workflow = pe.Workflow(name=name)
"""
Define the inputs to this workflow
"""
inputnode = pe.Node(niu.IdentityInterface(fields=[
'functionals', 'subject_id', 'subjects_dir', 'fwhm', 'norm_threshold',
'zintensity_threshold', 'tr', 'do_slicetime', 'sliceorder', 'node',
'csf_prob', 'wm_prob', 'gm_prob'
]),
name='inputspec')
"""
Setup the processing nodes and create the mask generation and coregistration
workflow
"""
poplist = lambda x: x.pop()
#realign = pe.Node(spm.Realign(), name='realign')
sym_func = pe.Node(niu.Function(input_names=['in_file'],
output_names=['out_link'],
function=do_symlink),
name='func_symlink')
realign = pe.Node(niu.Function(
input_names=['node', 'in_file', 'tr', 'do_slicetime', 'sliceorder'],
output_names=['out_file', 'par_file'],
function=mod_realign),
name="mod_realign")
mean = art_mean_workflow()
workflow.connect(realign, 'out_file', mean, 'inputspec.realigned_files')
workflow.connect(realign, 'par_file', mean,
'inputspec.realignment_parameters')
mean.inputs.inputspec.parameter_source = 'FSL' # Modular realign puts it in FSL format for consistency
#workflow.connect(inputnode, 'functionals', realign, 'in_file')
workflow.connect(inputnode, 'functionals', sym_func, 'in_file')
workflow.connect(sym_func, 'out_link', realign, 'in_file')
workflow.connect(inputnode, 'tr', realign, 'tr')
workflow.connect(inputnode, 'do_slicetime', realign, 'do_slicetime')
workflow.connect(inputnode, 'sliceorder', realign, 'sliceorder')
workflow.connect(inputnode, 'node', realign, 'node')
maskflow = create_getmask_flow()
workflow.connect([(inputnode, maskflow,
[('subject_id', 'inputspec.subject_id'),
('subjects_dir', 'inputspec.subjects_dir')])])
maskflow.inputs.inputspec.contrast_type = 't2'
workflow.connect(mean, 'outputspec.mean_image', maskflow,
'inputspec.source_file')
smooth = pe.Node(spm.Smooth(), name='smooth')
normalize = pe.Node(spm.Normalize(jobtype='write'), name='normalize')
normalize_struct = normalize.clone('normalize_struct')
segment = pe.Node(spm.Segment(csf_output_type=[True, True, False],
gm_output_type=[True, True, False],
wm_output_type=[True, True, False]),
name='segment')
mergefunc = lambda in1, in2, in3: [in1, in2, in3]
# merge = pe.Node(niu.Merge(),name='merge')
merge = pe.Node(niu.Function(input_names=['in1', 'in2', 'in3'],
output_names=['out'],
function=mergefunc),
name='merge')
workflow.connect(inputnode, 'csf_prob', merge, 'in3')
workflow.connect(inputnode, 'wm_prob', merge, 'in2')
workflow.connect(inputnode, 'gm_prob', merge, 'in1')
#workflow.connect(merge,'out', segment,'tissue_prob_maps')
sym_prob = sym_func.clone('sym_prob')
workflow.connect(merge, 'out', sym_prob, 'in_file')
workflow.connect(sym_prob, 'out_link', segment, 'tissue_prob_maps')
workflow.connect(maskflow, ('outputspec.mask_file', pickfirst), segment,
'mask_image')
workflow.connect(inputnode, 'fwhm', smooth, 'fwhm')
#sym_brain = sym_func.clone('sym_brain')
#workflow.connect(realign, 'mean_image', normalize, 'source')
#workflow.connect(maskflow,'fssource.brain',segment,'data')
fssource = maskflow.get_node('fssource')
import nipype.interfaces.freesurfer as fs
convert_brain = pe.Node(interface=fs.ApplyVolTransform(inverse=True),
name='convert')
workflow.connect(fssource, 'brain', convert_brain, 'target_file')
workflow.connect(maskflow, ('outputspec.reg_file', pickfirst),
convert_brain, 'reg_file')
workflow.connect(mean, 'outputspec.mean_image', convert_brain,
'source_file')
convert2nii = pe.Node(fs.MRIConvert(in_type='mgz', out_type='nii'),
name='convert2nii')
workflow.connect(convert_brain, 'transformed_file', convert2nii, 'in_file')
workflow.connect(convert2nii, 'out_file', segment, 'data')
workflow.connect(segment, 'transformation_mat', normalize,
'parameter_file')
workflow.connect(segment, 'transformation_mat', normalize_struct,
'parameter_file')
workflow.connect(convert2nii, 'out_file', normalize_struct,
'apply_to_files')
workflow.connect(realign, 'out_file', normalize, 'apply_to_files')
#normalize.inputs.template='/software/spm8/templates/EPI.nii'
workflow.connect(normalize, 'normalized_files', smooth, 'in_files')
#workflow.connect(realign, 'realigned_files', smooth, 'in_files')
artdetect = pe.Node(ra.ArtifactDetect(mask_type='file',
parameter_source='FSL',
use_differences=[True, False],
use_norm=True,
save_plot=True),
name='artdetect')
workflow.connect([(inputnode, artdetect,
[('norm_threshold', 'norm_threshold'),
('zintensity_threshold', 'zintensity_threshold')])])
workflow.connect([(realign, artdetect, [('out_file', 'realigned_files'),
('par_file',
'realignment_parameters')])])
workflow.connect(maskflow, ('outputspec.mask_file', poplist), artdetect,
'mask_file')
"""
Define the outputs of the workflow and connect the nodes to the outputnode
"""
outputnode = pe.Node(niu.IdentityInterface(fields=[
"realignment_parameters", "smoothed_files", "mask_file", "mean_image",
"reg_file", "reg_cost", 'outlier_files', 'outlier_stats',
'outlier_plots', 'norm_components', 'mod_csf', 'unmod_csf', 'mod_wm',
'unmod_wm', 'mod_gm', 'unmod_gm', 'mean', 'normalized_struct',
'struct_in_functional_space', 'normalization_parameters',
'reverse_normalize_parameters'
]),
name="outputspec")
workflow.connect([
(maskflow, outputnode, [("outputspec.reg_file", "reg_file")]),
(maskflow, outputnode, [("outputspec.reg_cost", "reg_cost")]),
(maskflow, outputnode, [(("outputspec.mask_file", poplist),
"mask_file")]),
(realign, outputnode, [('par_file', 'realignment_parameters')]),
(smooth, outputnode, [('smoothed_files', 'smoothed_files')]),
(artdetect, outputnode, [('outlier_files', 'outlier_files'),
('statistic_files', 'outlier_stats'),
('plot_files', 'outlier_plots'),
('norm_files', 'norm_components')])
])
workflow.connect(segment, 'modulated_csf_image', outputnode, 'mod_csf')
workflow.connect(segment, 'modulated_wm_image', outputnode, 'mod_wm')
workflow.connect(segment, 'modulated_gm_image', outputnode, 'mod_gm')
workflow.connect(segment, 'normalized_csf_image', outputnode, 'unmod_csf')
workflow.connect(segment, 'normalized_wm_image', outputnode, 'unmod_wm')
workflow.connect(segment, 'normalized_gm_image', outputnode, 'unmod_gm')
workflow.connect(mean, 'outputspec.mean_image', outputnode, 'mean')
workflow.connect(normalize_struct, 'normalized_files', outputnode,
'normalized_struct')
workflow.connect(segment, 'transformation_mat', outputnode,
'normalization_parameters')
workflow.connect(segment, 'inverse_transformation_mat', outputnode,
'reverse_normalize_parameters')
workflow.connect(convert2nii, 'out_file', outputnode,
'struct_in_functional_space')
workflow.inputs.inputspec.fwhm = c.fwhm
workflow.inputs.inputspec.subjects_dir = c.surf_dir
workflow.inputs.inputspec.norm_threshold = c.norm_thresh
workflow.inputs.inputspec.zintensity_threshold = c.z_thresh
workflow.inputs.inputspec.node = c.motion_correct_node
workflow.inputs.inputspec.tr = c.TR
workflow.inputs.inputspec.do_slicetime = c.do_slicetiming
workflow.inputs.inputspec.sliceorder = c.SliceOrder
workflow.inputs.inputspec.csf_prob = c.csf_prob
workflow.inputs.inputspec.gm_prob = c.grey_prob
workflow.inputs.inputspec.wm_prob = c.white_prob
workflow.base_dir = c.working_dir
workflow.config = {'execution': {'crashdump_dir': c.crash_dir}}
datagrabber = get_dataflow(c)
workflow.connect(datagrabber, 'func', inputnode, 'functionals')
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id']),
name='subject_names')
if not c.test_mode:
infosource.iterables = ('subject_id', c.subjects)
else:
infosource.iterables = ('subject_id', c.subjects[:1])
workflow.connect(infosource, 'subject_id', inputnode, 'subject_id')
workflow.connect(infosource, 'subject_id', datagrabber, 'subject_id')
sub = lambda x: [('_subject_id_%s' % x, '')]
sinker = pe.Node(nio.DataSink(), name='sinker')
workflow.connect(infosource, 'subject_id', sinker, 'container')
workflow.connect(infosource, ('subject_id', sub), sinker, 'substitutions')
sinker.inputs.base_directory = c.sink_dir
outputspec = workflow.get_node('outputspec')
workflow.connect(outputspec, 'realignment_parameters', sinker,
'spm_preproc.realignment_parameters')
workflow.connect(outputspec, 'smoothed_files', sinker,
'spm_preproc.smoothed_outputs')
workflow.connect(outputspec, 'outlier_files', sinker,
'spm_preproc.art.@outlier_files')
workflow.connect(outputspec, 'outlier_stats', sinker,
'spm_preproc.art.@outlier_stats')
workflow.connect(outputspec, 'outlier_plots', sinker,
'spm_preproc.art.@outlier_plots')
workflow.connect(outputspec, 'norm_components', sinker,
'spm_preproc.art.@norm')
workflow.connect(outputspec, 'reg_file', sinker,
'spm_preproc.bbreg.@reg_file')
workflow.connect(outputspec, 'reg_cost', sinker,
'spm_preproc.bbreg.@reg_cost')
workflow.connect(outputspec, 'mask_file', sinker,
'spm_preproc.mask.@mask_file')
workflow.connect(outputspec, 'mod_csf', sinker,
'spm_preproc.segment.mod.@csf')
workflow.connect(outputspec, 'mod_wm', sinker,
'spm_preproc.segment.mod.@wm')
workflow.connect(outputspec, 'mod_gm', sinker,
'spm_preproc.segment.mod.@gm')
workflow.connect(outputspec, 'unmod_csf', sinker,
'spm_preproc.segment.unmod.@csf')
workflow.connect(outputspec, 'unmod_wm', sinker,
'spm_preproc.segment.unmod.@wm')
workflow.connect(outputspec, 'unmod_gm', sinker,
'spm_preproc.segment.unmod.@gm')
workflow.connect(outputspec, 'mean', sinker, 'spm_preproc.mean')
workflow.connect(outputspec, 'normalized_struct', sinker,
'spm_preproc.normalized_struct')
workflow.connect(outputspec, 'normalization_parameters', sinker,
'spm_preproc.normalization_parameters.@forward')
workflow.connect(outputspec, 'reverse_normalize_parameters', sinker,
'spm_preproc.normalization_parameters.@reverse')
workflow.connect(outputspec, 'struct_in_functional_space', sinker,
'spm_preproc.struct_in_func_space')
return workflow
coregister.iterables = ('target', 'func')
coregister.inputs.source = 't2.nii'
coregister2 = pe.Node(interface=spm.Coregister(), name="coregister2")
coregister2.inputs.jobtype = 'estimate' # coreg output of T2 and T2* to T1
coregister2.iterables = ('target', ['func','t2.nii'])
coregister2.inputs.source = 't1.nii'
## old segment
# Q: why old?
## old normalize
# prefix = w (norm'd to MNI)
normalize = pe.Node(interface=spm.Normalize(), name="normalize") # Q: is this old norm?
normalize.inputs.template = os.path.abspath('data/T1.nii') # Q: dir of MNI?
## smooth
# 8 fwhm
smooth = pe.Node(interface=spm.Smooth(), name="smooth")
smooth.iterables = ('fwhm', [8])
## set up pipeline
preproc_pipeline = pe.Workflow(name="preproc")
preproc_pipeline.base_dir = os.path.abspath('spm_tutorial/workingdir') #Q: dir?
preproc_pipeline.connect([(infosource, datasource, [('subject_id', 'subject_id')]),
def spm_register_to_template_wf(wf_name="spm_registration_to_template"):
"""Return a workflow that registers each reg_input.in_file to the file in reg_input.template.
For now this does not do atlas registration.
It does:
- SPM12 Warp input image to the given template
Parameters
----------
wf_name: str
Name of the workflow.
Nipype Inputs
-------------
reg_input.in_file: traits.File
The raw NIFTI_GZ subject image file.
reg_input.template: list of traits.File
The template file for inter-subject registration reference.
Nipype outputs
--------------
reg_output.warped: existing file
Image normalized to the given template.
reg_output.warp_field: existing files
Spatial normalization parameters .mat file.
Returns
-------
wf: nipype Workflow
"""
# specify input and output fields
in_fields = [
"in_file",
"template",
]
out_fields = [
"warped",
"warp_field",
]
# input
reg_input = setup_node(IdentityInterface(fields=in_fields,
mandatory_inputs=True),
name="reg_input")
# warp each subject to the group template
gunzip_template = setup_node(
Gunzip(),
name="gunzip_template",
)
gunzip_input = setup_node(
Gunzip(),
name="gunzip_input",
)
warp2template = setup_node(spm.Normalize(jobtype="estwrite",
out_prefix="wgrptemplate_"),
name="warp2template")
get_bbox = setup_node(Function(function=get_bounding_box,
input_names=["in_file"],
output_names=["bbox"]),
name="get_bbox")
# output
reg_output = setup_node(IdentityInterface(fields=out_fields),
name="reg_output")
# Create the workflow object
wf = pe.Workflow(name=wf_name)
wf.connect([
# get template bounding box to apply to results
(reg_input, get_bbox, [("template", "in_file")]),
# gunzip some inputs
(reg_input, gunzip_input, [("in_file", "in_file")]),
(reg_input, gunzip_template, [("template", "in_file")]),
# prepare the target parameters of the warp to template
(gunzip_template, warp2template, [("out_file", "template")]),
(get_bbox, warp2template, [("bbox", "write_bounding_box")]),
# directly warp pet to the template
(gunzip_input, warp2template, [("out_file", "source")]),
# output
(warp2template, reg_output, [
("normalization_parameters", "warp_field"),
("normalized_source", "warped"),
]),
])
return wf
def __init__(self, func_source, struct_source, datasink):
# specify input and output nodes
self.func_source = func_source
self.struct_source = struct_source
self.datasink = datasink
# specify nodes
# structual process
self.bet_struct = pe.Node(interface=fsl.BET(),
name='non_brain_removal_BET_struct')
self.bet_struct.inputs.output_type = "NIFTI"
# functional process
self.slice_timer = pe.Node(interface=fsl.SliceTimer(),
name='time_slice_correction')
self.mcflirt = pe.Node(interface=fsl.MCFLIRT(),
name='motion_correction')
self.mcflirt.inputs.output_type = "NIFTI"
self.mcflirt.inputs.mean_vol = True
self.fslsplit = pe.Node(interface=fsl.Split(), name='fslsplit')
self.fslsplit.inputs.dimension = 't'
self.fslsplit.inputs.output_type = "NIFTI"
self.fslmerge = pe.Node(interface=fsl.Merge(), name='fslmerge')
self.fslmerge.inputs.dimension = 't'
self.fslmerge.inputs.output_type = "NIFTI"
self.bet_mean = pe.Node(interface=fsl.BET(),
name='non_brain_removal_BET_mean')
self.bet_mean.inputs.output_type = "NIFTI"
# helper function(s)
def bet_each(in_files):
'''
@param in_files: list of image files
@return out_files: list of image files after applied fsl.BET on it
'''
from nipype.interfaces import fsl
import nipype.pipeline.engine as pe
out_files = list()
step_no = 0
for file_ in in_files:
bet = pe.Node(interface=fsl.BET(),
name='BET_for_step_{}'.format(step_no))
bet.inputs.in_file = file_
bet.inputs.out_file = file_[:len(file_) - 4] + '_bet.nii'
bet.inputs.output_type = "NIFTI"
bet.run()
out_files.append(bet.inputs.out_file)
step_no += 1
return out_files
# bet_func return a list of NIFITI files
self.bet_func = pe.Node(interface=Function(input_names=['in_files'],
output_names=['out_files'],
function=bet_each),
name='non_brain_removal_BET_func')
self.coregister = pe.Node(interface=spm.Coregister(),
name="coregister")
self.coregister.inputs.jobtype = 'estimate'
self.segment = pe.Node(interface=spm.Segment(), name="segment")
self.segment.inputs.affine_regularization = 'mni'
self.normalize_func = pe.Node(interface=spm.Normalize(),
name="normalize_func")
self.normalize_func.inputs.jobtype = "write"
# self.fourier = pe.Node(interface=afni.Fourier(), name='temporal_filtering')
# self.fourier.inputs.highpass = 0.01
# self.fourier.inputs.lowpass = 0.1
self.smooth = pe.Node(interface=spm.Smooth(), name="smooth")
self.smooth.inputs.fwhm = [8, 8, 8]
# specify workflow instance
self.workflow = pe.Workflow(name='preprocessing_workflow')
# connect nodes
self.workflow.connect([
(self.struct_source, self.bet_struct, [('outfiles', 'in_file')]),
(self.func_source, self.slice_timer, [('outfiles', 'in_file')]),
(self.slice_timer, self.mcflirt, [('slice_time_corrected_file',
'in_file')]),
(self.mcflirt, self.bet_mean, [('mean_img', 'in_file')]),
(self.mcflirt, self.fslsplit, [('out_file', 'in_file')]),
(self.fslsplit, self.bet_func, [('out_files', 'in_files')]),
(self.bet_func, self.fslmerge, [('out_files', 'in_files')
]), # intersect
(self.bet_struct, self.coregister, [('out_file', 'source')]),
(self.bet_mean, self.coregister, [('out_file', 'target')]),
(self.coregister, self.segment, [('coregistered_source', 'data')]),
(self.segment, self.normalize_func, [('transformation_mat',
'parameter_file')]),
(self.fslmerge, self.normalize_func, [('merged_file',
'apply_to_files')]),
(self.normalize_func, self.smooth, [('normalized_files',
'in_files')]),
(self.coregister, self.datasink, [('coregistered_source',
'registered_file')]),
(self.normalize_func, self.datasink, [('normalized_files',
'before_smooth')]),
(self.smooth, self.datasink, [('smoothed_files', 'final_out')])
])
def test_normalize():
yield assert_equal, spm.Normalize._jobtype, 'spatial'
yield assert_equal, spm.Normalize._jobname, 'normalise'
yield assert_equal, spm.Normalize().inputs.jobtype, 'estwrite'
"""
Use :class:`nipype.interfaces.freesurfer.ApplyVolTransform` to convert contrast
images into freesurfer space.
"""
normwreg = pe.MapNode(interface=fs.ApplyVolTransform(),
iterfield=['source_file'],
name='applyreg2con')
"""
Use :class:`nipype.interfaces.spm.Normalize` to normalize the contrast images
to MNI space
"""
normalize = pe.Node(interface=spm.Normalize(jobtype='write'),
name='norm2mni')
"""
Connect up the volume normalization components
"""
volnorm.connect([(convert, segment, [('out_file','data')]),
(convert2, normwreg, [('out_file', 'source_file')]),
(segment, normalize, [('transformation_mat', 'parameter_file')]),
(normwreg, normalize, [('transformed_file','apply_to_files')]),
])
"""
Preproc + Analysis + VolumeNormalization workflow
-------------------------------------------------
def spm_warp_fmri_wf(wf_name="spm_warp_fmri", register_to_grptemplate=False):
""" Run SPM to warp resting-state fMRI pre-processed data to MNI or a given
template.
Tasks:
- Warping the inputs to MNI or a template, if `do_group_template` is True
Parameters
----------
wf_name: str
register_to_grptemplate: bool
If True will expect the wfmri_input.epi_template input and use it as a group template
for inter-subject registratio.
Nipype Inputs
-------------
wfmri_input.in_file: traits.File
The slice time and motion corrected fMRI file.
wfmri_input.reference_file: traits.File
The anatomical image in its native space
for registration reference.
wfmri_input.anat_fmri: traits.File
The anatomical image in fMRI space.
wfmri_input.anat_to_mni_warp: traits.File
The warp field from the transformation of the
anatomical image to the standard MNI space.
wfmri_input.time_filtered: traits.File
The bandpass time filtered fMRI file.
wfmri_input.avg_epi: traits.File
The average EPI from the fMRI file.
wfmri_input.epi_template: traits.File
Reference EPI template file for inter subject registration.
If `do_group_template` is True you must specify this input.
wfmri_input.brain_mask: traits.File
Brain mask in fMRI space.
wfmri_input.atlas_anat: traits.File
Atlas in subject anatomical space.
Nipype Outputs
--------------
wfmri_output.warped_fmri: traits.File
The slice time, motion, and nuisance corrected fMRI
file registered to the template.
wfmri_output.wtime_filtered: traits.File
The bandpass time filtered fMRI file
registered to the template.
wfmri_output.smooth: traits.File
The smooth bandpass time filtered fMRI file
registered to the template.
wfmri_output.wavg_epi: traits.File
The average EPI from the fMRI file
registered to the template.
wfmri_output.warp_field: traits.File
The fMRI to template warp field.
wfmri_output.coreg_avg_epi: traits.File
The average EPI image in anatomical space.
Only if registration.anat2fmri is false.
wfmri_output.coreg_others: traits.File
Other mid-preprocessing fmri images registered to
anatomical space:
- wfmri_input.in_file,
- wfmri_input.brain_mask,
- wfmri_input.time_filtered.
Only if registration.anat2fmri is false
wfmri_output.wbrain_mask: traits.File
Brain mask in fMRI space warped to MNI.
Returns
-------
wf: nipype Workflow
"""
# Create the workflow object
wf = pe.Workflow(name=wf_name)
# specify input and output fields
in_fields = ["in_file",
"anat_fmri",
"anat_to_mni_warp",
"brain_mask",
"reference_file",
"time_filtered",
"avg_epi",]
out_fields = ["warped_fmri",
"wtime_filtered",
"smooth",
"wavg_epi",
"wbrain_mask",
"warp_field",
"coreg_avg_epi",
"coreg_others"
]
if register_to_grptemplate:
in_fields += ['epi_template']
do_atlas, _ = check_atlas_file()
if do_atlas:
in_fields += ["atlas_anat"]
out_fields += ["atlas_fmri"]
# input identities
wfmri_input = setup_node(IdentityInterface(fields=in_fields, mandatory_inputs=True),
name="wfmri_input")
# in file unzipper
in_gunzip = pe.Node(Gunzip(), name="in_gunzip")
# merge list for normalization input
merge_list = pe.Node(Merge(2), name='merge_for_warp')
gunzipper = pe.MapNode(Gunzip(), name="gunzip", iterfield=['in_file'])
# the template bounding box
tpm_bbox = setup_node(Function(function=get_bounding_box,
input_names=["in_file"],
output_names=["bbox"]),
name="tpm_bbox")
# smooth the final result
smooth = setup_node(fsl.IsotropicSmooth(fwhm=8, output_type='NIFTI'), name="smooth_fmri")
# output identities
rest_output = setup_node(IdentityInterface(fields=out_fields),
name="wfmri_output")
# check how to perform the registration, to decide how to build the pipeline
anat2fmri = get_config_setting('registration.anat2fmri', False)
# register to group template
if register_to_grptemplate:
gunzip_template = pe.Node(Gunzip(), name="gunzip_template",)
warp = setup_node(spm.Normalize(jobtype="estwrite", out_prefix="wgrptmpl_"),
name="fmri_grptemplate_warp",)
warp_source_arg = "source"
warp_outsource_arg = "normalized_source"
warp_field_arg = "normalization_parameters"
elif anat2fmri:
# register to standard template
warp = setup_node(spm_normalize(), name="fmri_warp")
tpm_bbox.inputs.in_file = spm_tpm_priors_path()
warp_source_arg = "image_to_align"
warp_outsource_arg = "normalized_image"
warp_field_arg = "deformation_field"
else: # anat2fmri is False
coreg = setup_node(spm_coregister(cost_function="mi"), name="coreg_fmri")
warp = setup_node(spm_apply_deformations(), name="fmri_warp")
coreg_files = pe.Node(Merge(3), name='merge_for_coreg')
warp_files = pe.Node(Merge(2), name='merge_for_warp')
tpm_bbox.inputs.in_file = spm_tpm_priors_path()
# make the connections
if register_to_grptemplate:
wf.connect([
# get template bounding box to apply to results
(wfmri_input, tpm_bbox, [("epi_template", "in_file")]),
# unzip and forward the template file
(wfmri_input, gunzip_template, [("epi_template", "in_file")]),
(gunzip_template, warp, [("out_file", "template")]),
# get template bounding box to apply to results
(wfmri_input, tpm_bbox, [("epi_template", "in_file")]),
])
if anat2fmri or register_to_grptemplate:
# prepare the inputs
wf.connect([
# unzip the in_file input file
(wfmri_input, in_gunzip, [("avg_epi", "in_file")]),
# warp source file
(in_gunzip, warp, [("out_file", warp_source_arg)]),
# bounding box
(tpm_bbox, warp, [("bbox", "write_bounding_box")]),
# merge the other input files into a list
(wfmri_input, merge_list, [("in_file", "in1"),
("time_filtered", "in2"),
]),
# gunzip them for SPM
(merge_list, gunzipper, [("out", "in_file")]),
# apply to files
(gunzipper, warp, [("out_file", "apply_to_files")]),
# outputs
(warp, rest_output, [(warp_field_arg, "warp_field"),
(warp_outsource_arg, "wavg_epi"),
]),
])
else: # FMRI to ANAT
wf.connect([
(wfmri_input, coreg, [("reference_file", "target")]),
# unzip the in_file input file
(wfmri_input, in_gunzip, [("avg_epi", "in_file")]),
(in_gunzip, coreg, [("out_file", "source")]),
# merge the other input files into a list
(wfmri_input, coreg_files, [("in_file", "in1"),
("time_filtered", "in2"),
("brain_mask", "in3"),
]),
# gunzip them for SPM
(coreg_files, gunzipper, [("out", "in_file")]),
# coregister fmri to anat
(gunzipper, coreg, [("out_file", "apply_to_files")]),
# anat to mni warp field
(wfmri_input, warp, [("anat_to_mni_warp", "deformation_file")]),
# bounding box
(tpm_bbox, warp, [("bbox", "write_bounding_box")]),
# apply to files
(coreg, warp_files, [("coregistered_source", "in1")]),
(coreg, warp_files, [("coregistered_files", "in2")]),
(warp_files, warp, [("out", "apply_to_files")]),
# outputs
(warp, rest_output, [("normalized_files", "warped_files"),]),
(warp, rest_output, [(("normalized_files", selectindex, 0), "wavg_epi"),]),
(coreg, rest_output, [("coregistered_source", "coreg_avg_epi")]),
(coreg, rest_output, [("coregistered_files", "coreg_others")]),
])
# atlas file in fMRI space
if anat2fmri:
coreg_atlas = setup_node(spm_coregister(cost_function="mi"), name="coreg_atlas2fmri")
# set the registration interpolation to nearest neighbour.
coreg_atlas.inputs.write_interp = 0
wf.connect([
(wfmri_input, coreg_atlas, [("reference_file", "source"),
("atlas_anat", "apply_to_files"),
]),
(in_gunzip, coreg_atlas, [("out_file", "target")]),
(coreg_atlas, rest_output, [("coregistered_files", "atlas_fmri")]),
])
# smooth and sink
wf.connect([
# smooth the final bandpassed image
(warp, smooth, [(("normalized_files", selectindex, 1), "in_file")]),
# output
(smooth, rest_output, [("out_file", "smooth")]),
(warp, rest_output, [(("normalized_files", selectindex, 0), "warped_fmri"),
(("normalized_files", selectindex, 1), "wtime_filtered"),
]),
])
return wf
coregister = pe.Node(interface=spm.Coregister(), name="coregister") coregister.inputs.jobtype = 'estimate' segment = pe.Node(interface=spm.Segment(), name="segment") segment.inputs.save_bias_corrected = True """Uncomment the following line for faster execution """ # segment.inputs.gaussians_per_class = [1, 1, 1, 4] """Warp functional and structural data to SPM's T1 template using :class:`nipype.interfaces.spm.Normalize`. The tutorial data set includes the template image, T1.nii. """ normalize_func = pe.Node(interface=spm.Normalize(), name="normalize_func") normalize_func.inputs.jobtype = "write" normalize_struc = pe.Node(interface=spm.Normalize(), name="normalize_struc") normalize_struc.inputs.jobtype = "write" """Smooth the functional data using :class:`nipype.interfaces.spm.Smooth`. """ smooth = pe.Node(interface=spm.Smooth(), name="smooth") """`write_voxel_sizes` is the input of the normalize interface that is recommended to be set to the voxel sizes of the target volume. There is no need to set it manually since we van infer it from data using the following function: """
def create_spm_preproc(c, name='preproc'):
"""
"""
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
import nipype.algorithms.rapidart as ra
import nipype.interfaces.spm as spm
import nipype.interfaces.utility as niu
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
import nipype.interfaces.freesurfer as fs
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=[
'functionals', 'subject_id', 'subjects_dir', 'fwhm', 'norm_threshold',
'zintensity_threshold', 'tr', 'do_slicetime', 'sliceorder',
'parameters', 'node', 'csf_prob', 'wm_prob', 'gm_prob'
]),
name='inputspec')
poplist = lambda x: x.pop()
sym_func = pe.Node(niu.Function(input_names=['in_file'],
output_names=['out_link'],
function=do_symlink),
name='func_symlink')
# REALIGN
realign = pe.Node(niu.Function(
input_names=[
'node', 'in_file', 'tr', 'do_slicetime', 'sliceorder', 'parameters'
],
output_names=['out_file', 'par_file', 'parameter_source'],
function=mod_realign),
name="mod_realign")
workflow.connect(inputnode, 'parameters', realign, 'parameters')
workflow.connect(inputnode, 'functionals', realign, 'in_file')
workflow.connect(inputnode, 'tr', realign, 'tr')
workflow.connect(inputnode, 'do_slicetime', realign, 'do_slicetime')
workflow.connect(inputnode, 'sliceorder', realign, 'sliceorder')
workflow.connect(inputnode, 'node', realign, 'node')
# TAKE MEAN IMAGE
mean = art_mean_workflow()
workflow.connect(realign, 'out_file', mean, 'inputspec.realigned_files')
workflow.connect(realign, 'par_file', mean,
'inputspec.realignment_parameters')
workflow.connect(realign, 'parameter_source', mean,
'inputspec.parameter_source')
# CREATE BRAIN MASK
maskflow = create_getmask_flow()
workflow.connect([(inputnode, maskflow,
[('subject_id', 'inputspec.subject_id'),
('subjects_dir', 'inputspec.subjects_dir')])])
maskflow.inputs.inputspec.contrast_type = 't2'
workflow.connect(mean, 'outputspec.mean_image', maskflow,
'inputspec.source_file')
# SEGMENT
segment = pe.Node(spm.Segment(csf_output_type=[True, True, False],
gm_output_type=[True, True, False],
wm_output_type=[True, True, False]),
name='segment')
mergefunc = lambda in1, in2, in3: [in1, in2, in3]
merge = pe.Node(niu.Function(input_names=['in1', 'in2', 'in3'],
output_names=['out'],
function=mergefunc),
name='merge')
workflow.connect(inputnode, 'csf_prob', merge, 'in3')
workflow.connect(inputnode, 'wm_prob', merge, 'in2')
workflow.connect(inputnode, 'gm_prob', merge, 'in1')
sym_prob = sym_func
workflow.connect(merge, 'out', sym_prob, 'in_file')
workflow.connect(sym_prob, 'out_link', segment, 'tissue_prob_maps')
xform_mask = pe.Node(fs.ApplyVolTransform(fs_target=True),
name='transform_mask')
workflow.connect(maskflow, ('outputspec.reg_file', pickfirst), xform_mask,
'reg_file')
workflow.connect(maskflow, ('outputspec.mask_file', pickfirst), xform_mask,
'source_file')
workflow.connect(xform_mask, "transformed_file", segment, 'mask_image')
fssource = maskflow.get_node('fssource')
convert2nii = pe.Node(fs.MRIConvert(in_type='mgz', out_type='nii'),
name='convert2nii')
workflow.connect(fssource, 'brain', convert2nii, 'in_file')
workflow.connect(convert2nii, 'out_file', segment, 'data')
# NORMALIZE
normalize = pe.MapNode(spm.Normalize(jobtype='write'),
name='normalize',
iterfield=['apply_to_files'])
normalize_struct = normalize.clone('normalize_struct')
normalize_mask = normalize.clone('normalize_mask')
workflow.connect(segment, 'transformation_mat', normalize,
'parameter_file')
workflow.connect(segment, 'transformation_mat', normalize_mask,
'parameter_file')
workflow.connect(segment, 'transformation_mat', normalize_struct,
'parameter_file')
workflow.connect(convert2nii, 'out_file', normalize_struct,
'apply_to_files')
workflow.connect(xform_mask, "transformed_file", normalize_mask,
'apply_to_files')
xform_image = pe.MapNode(fs.ApplyVolTransform(fs_target=True),
name='xform_image',
iterfield=['source_file'])
workflow.connect(maskflow, ('outputspec.reg_file', pickfirst), xform_image,
'reg_file')
workflow.connect(realign, 'out_file', xform_image, "source_file")
workflow.connect(xform_image, "transformed_file", normalize,
"apply_to_files")
#SMOOTH
smooth = pe.Node(spm.Smooth(), name='smooth')
workflow.connect(inputnode, 'fwhm', smooth, 'fwhm')
workflow.connect(normalize, 'normalized_files', smooth, 'in_files')
# ART
artdetect = pe.Node(ra.ArtifactDetect(mask_type='file',
use_differences=[True, False],
use_norm=True,
save_plot=True),
name='artdetect')
workflow.connect(realign, 'parameter_source', artdetect,
'parameter_source')
workflow.connect([(inputnode, artdetect,
[('norm_threshold', 'norm_threshold'),
('zintensity_threshold', 'zintensity_threshold')])])
workflow.connect([(realign, artdetect, [('out_file', 'realigned_files'),
('par_file',
'realignment_parameters')])])
workflow.connect(maskflow, ('outputspec.mask_file', poplist), artdetect,
'mask_file')
# OUTPUTS
outputnode = pe.Node(niu.IdentityInterface(fields=[
"realignment_parameters", "smoothed_files", "mask_file", "mean_image",
"reg_file", "reg_cost", 'outlier_files', 'outlier_stats',
'outlier_plots', 'norm_components', 'mod_csf', 'unmod_csf', 'mod_wm',
'unmod_wm', 'mod_gm', 'unmod_gm', 'mean', 'normalized_struct',
'normalization_parameters', 'reverse_normalize_parameters'
]),
name="outputspec")
workflow.connect([
(maskflow, outputnode, [("outputspec.reg_file", "reg_file")]),
(maskflow, outputnode, [("outputspec.reg_cost", "reg_cost")]),
(realign, outputnode, [('par_file', 'realignment_parameters')]),
(smooth, outputnode, [('smoothed_files', 'smoothed_files')]),
(artdetect, outputnode, [('outlier_files', 'outlier_files'),
('statistic_files', 'outlier_stats'),
('plot_files', 'outlier_plots'),
('norm_files', 'norm_components')])
])
workflow.connect(normalize_mask, "normalized_files", outputnode,
"mask_file")
workflow.connect(segment, 'modulated_csf_image', outputnode, 'mod_csf')
workflow.connect(segment, 'modulated_wm_image', outputnode, 'mod_wm')
workflow.connect(segment, 'modulated_gm_image', outputnode, 'mod_gm')
workflow.connect(segment, 'normalized_csf_image', outputnode, 'unmod_csf')
workflow.connect(segment, 'normalized_wm_image', outputnode, 'unmod_wm')
workflow.connect(segment, 'normalized_gm_image', outputnode, 'unmod_gm')
workflow.connect(mean, 'outputspec.mean_image', outputnode, 'mean')
workflow.connect(normalize_struct, 'normalized_files', outputnode,
'normalized_struct')
workflow.connect(segment, 'transformation_mat', outputnode,
'normalization_parameters')
workflow.connect(segment, 'inverse_transformation_mat', outputnode,
'reverse_normalize_parameters')
# CONNECT TO CONFIG
workflow.inputs.inputspec.fwhm = c.fwhm
workflow.inputs.inputspec.subjects_dir = c.surf_dir
workflow.inputs.inputspec.norm_threshold = c.norm_thresh
workflow.inputs.inputspec.zintensity_threshold = c.z_thresh
workflow.inputs.inputspec.node = c.motion_correct_node
workflow.inputs.inputspec.tr = c.TR
workflow.inputs.inputspec.do_slicetime = c.do_slicetiming
workflow.inputs.inputspec.sliceorder = c.SliceOrder
workflow.inputs.inputspec.csf_prob = c.csf_prob
workflow.inputs.inputspec.gm_prob = c.grey_prob
workflow.inputs.inputspec.wm_prob = c.white_prob
workflow.inputs.inputspec.parameters = {"order": c.order}
workflow.base_dir = c.working_dir
workflow.config = {'execution': {'crashdump_dir': c.crash_dir}}
datagrabber = get_dataflow(c)
workflow.connect(datagrabber, 'func', inputnode, 'functionals')
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id']),
name='subject_names')
if not c.test_mode:
infosource.iterables = ('subject_id', c.subjects)
else:
infosource.iterables = ('subject_id', c.subjects[:1])
workflow.connect(infosource, 'subject_id', inputnode, 'subject_id')
workflow.connect(infosource, 'subject_id', datagrabber, 'subject_id')
sub = lambda x: [('_subject_id_%s' % x, '')]
sinker = pe.Node(nio.DataSink(), name='sinker')
workflow.connect(infosource, 'subject_id', sinker, 'container')
workflow.connect(infosource, ('subject_id', sub), sinker, 'substitutions')
sinker.inputs.base_directory = c.sink_dir
outputspec = workflow.get_node('outputspec')
workflow.connect(outputspec, 'realignment_parameters', sinker,
'spm_preproc.realignment_parameters')
workflow.connect(outputspec, 'smoothed_files', sinker,
'spm_preproc.smoothed_outputs')
workflow.connect(outputspec, 'outlier_files', sinker,
'spm_preproc.art.@outlier_files')
workflow.connect(outputspec, 'outlier_stats', sinker,
'spm_preproc.art.@outlier_stats')
workflow.connect(outputspec, 'outlier_plots', sinker,
'spm_preproc.art.@outlier_plots')
workflow.connect(outputspec, 'norm_components', sinker,
'spm_preproc.art.@norm')
workflow.connect(outputspec, 'reg_file', sinker,
'spm_preproc.bbreg.@reg_file')
workflow.connect(outputspec, 'reg_cost', sinker,
'spm_preproc.bbreg.@reg_cost')
workflow.connect(outputspec, 'mask_file', sinker,
'spm_preproc.mask.@mask_file')
workflow.connect(outputspec, 'mod_csf', sinker,
'spm_preproc.segment.mod.@csf')
workflow.connect(outputspec, 'mod_wm', sinker,
'spm_preproc.segment.mod.@wm')
workflow.connect(outputspec, 'mod_gm', sinker,
'spm_preproc.segment.mod.@gm')
workflow.connect(outputspec, 'unmod_csf', sinker,
'spm_preproc.segment.unmod.@csf')
workflow.connect(outputspec, 'unmod_wm', sinker,
'spm_preproc.segment.unmod.@wm')
workflow.connect(outputspec, 'unmod_gm', sinker,
'spm_preproc.segment.unmod.@gm')
workflow.connect(outputspec, 'mean', sinker, 'spm_preproc.mean')
workflow.connect(outputspec, 'normalized_struct', sinker,
'spm_preproc.normalized_struct')
workflow.connect(outputspec, 'normalization_parameters', sinker,
'spm_preproc.normalization_parameters.@forward')
workflow.connect(outputspec, 'reverse_normalize_parameters', sinker,
'spm_preproc.normalization_parameters.@reverse')
return workflow