def calc(self,
in_file_a,
expr,
in_file_b=None,
in_file_c=None,
output=None,
suffix=None):
in_file_a, output = self.FuncHandler(in_file_a, output, suffix)
in_file_b, _ = self.FuncHandler(in_file_b, output, suffix)
in_file_c, _ = self.FuncHandler(in_file_c, output, suffix)
mycalc = afni.Calc(in_file_a=in_file_a,
in_file_b=in_file_b,
expr=expr,
out_file=output)
#https://nipype.readthedocs.io/en/latest/interfaces/generated/interfaces.afni/utils.html#calc
mycalc.inputs.outputtype = "NIFTI_GZ"
mycalc.inputs.num_threads = cpu_count()
mycalc.run()
for in_file in [in_file_a, in_file_b]:
if type(in_file) == models.BIDSImageFile:
in_file = os.path.join(self._output_dir, in_file.filename)
if "_desc-temp" in in_file:
os.remove(in_file)
def __init__(self, settings):
# call base constructor
super().__init__(settings)
# define input/output node
self.set_input(['refimg', 'T1_skullstrip'])
self.set_output(['affine_func_2_anat', 'warp_func_2_anat'])
# define datasink substitutions
self.set_subs([
('_calc_calc_calc_calc_calc', ''),
('_roi', '_reference'),
('_unwarped_Warped', '_unwarped'),
('_masked_calc', '_skullstrip'),
('_Warped', '_anat'),
])
# Skullstrip the EPI image
self.epi_skullstrip = Node(fsl.BET(), name='epi_skullstrip')
self.epi_automask = Node(afni.Automask(args='-overwrite',
outputtype='NIFTI_GZ'),
name='epi_automask')
self.epi_3dcalc = Node(afni.Calc(expr='c*or(a,b)',
overwrite=True,
outputtype='NIFTI_GZ'),
name='epi_3dcalc')
# create the output name for the registration
self.create_prefix = Node(Function(input_names=['filename'],
output_names=['basename'],
function=get_prefix),
name='create_prefix')
# align func to anat
self.align_func_2_anat = Node(ants.Registration(
num_threads=settings['num_threads'],
collapse_output_transforms=False,
initial_moving_transform_com=1,
write_composite_transform=True,
initialize_transforms_per_stage=True,
transforms=['Rigid', 'Affine'],
transform_parameters=[(0.1, ), (0.1, )],
metric=['MI', 'MI'],
metric_weight=[1, 1],
radius_or_number_of_bins=[32, 32],
sampling_strategy=['Regular', 'Regular'],
sampling_percentage=[0.25, 0.25],
convergence_threshold=[1.e-6, 1.e-8],
convergence_window_size=[10, 10],
smoothing_sigmas=[[3, 2, 1, 0], [2, 1, 0]],
sigma_units=['vox', 'vox'],
shrink_factors=[[8, 4, 2, 1], [4, 2, 1]],
number_of_iterations=[[1000, 500, 250, 100], [500, 250, 100]],
use_estimate_learning_rate_once=[False, True],
use_histogram_matching=False,
verbose=True,
output_warped_image=True),
name='align_func_2_anat')
self.align_func_2_anat.n_procs = settings['num_threads']
def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['label-reorient_T1w']]:
anat_image = rp[R('T1w', label='reorient')]
anat_skullstrip = NipypeJob(interface=afni.SkullStrip(
outputtype='NIFTI_GZ',
args=create_3dskullstrip_arg_string(**config)),
reference='anat_skullstrip')
anat_skullstrip.in_file = anat_image
anat_brain_mask = NipypeJob(interface=afni.Calc(expr='step(a)',
outputtype='NIFTI_GZ'),
reference='anat_brain_mask')
anat_skullstrip_orig_vol = NipypeJob(
interface=afni.Calc(expr='a*step(b)', outputtype='NIFTI_GZ'),
reference='anat_skullstrip_orig_vol')
anat_brain_mask.in_file_a = anat_skullstrip.out_file
anat_skullstrip_orig_vol.in_file_a = anat_image
anat_skullstrip_orig_vol.in_file_b = anat_brain_mask.out_file
rp[R('T1w', desc='skullstrip-afni',
suffix='mask')] = anat_brain_mask.out_file
rp[R('T1w', desc='skullstrip-afni',
suffix='brain')] = anat_skullstrip_orig_vol.out_file
def create_corr_ts(name='corr_ts'):
corr_ts = Workflow(name='corr_ts')
# Define nodes
inputnode = Node(util.IdentityInterface(fields=[
'ts',
'hc_mask',
]),
name='inputnode')
outputnode = Node(interface=util.IdentityInterface(
fields=['corrmap', 'corrmap_z', 'hc_ts']),
name='outputnode')
#extract mean time series of mask
mean_TS = MapNode(interface=fsl.ImageMeants(),
name="mean_TS",
iterfield='mask')
#iterate over using Eigenvalues or mean
#mean_TS.iterables = ("eig", [True, False])
#mean_TS.inputs.order = 1
#mean_TS.inputs.show_all = True
mean_TS.inputs.eig = False #use only mean of ROI
mean_TS.inputs.out_file = "TS.1D"
#calculate correlation of all voxels with seed voxel
corr_TS = MapNode(interface=afni.Fim(),
name='corr_TS',
iterfield='ideal_file')
corr_TS.inputs.out = 'Correlation'
corr_TS.inputs.out_file = "corr.nii.gz"
apply_FisherZ = MapNode(interface=afni.Calc(),
name="apply_FisherZ",
iterfield='in_file_a')
apply_FisherZ.inputs.expr = 'log((1+a)/(1-a))/2' #log = ln
apply_FisherZ.inputs.out_file = 'corr_Z.nii.gz'
apply_FisherZ.inputs.outputtype = "NIFTI"
corr_ts.connect([(inputnode, mean_TS, [('hc_mask', 'mask')]),
(inputnode, mean_TS, [('ts', 'in_file')]),
(mean_TS, outputnode, [('out_file', 'hc_ts')]),
(inputnode, corr_TS, [('ts', 'in_file')]),
(mean_TS, corr_TS, [('out_file', 'ideal_file')]),
(corr_TS, apply_FisherZ, [('out_file', 'in_file_a')]),
(corr_TS, outputnode, [('out_file', 'corrmap')]),
(apply_FisherZ, outputnode, [('out_file', 'corrmap_z')])])
return corr_ts
def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['label-reorient_T1w']]:
anat = rp[R('T1w', label='reorient')]
anat_skullstrip = NipypeJob(interface=fsl.BET(output_type='NIFTI_GZ',
**config),
reference='anat_skullstrip')
anat_skullstrip.in_file = anat
anat_skullstrip_orig_vol = NipypeJob(
interface=afni.Calc(expr='a*step(b)', outputtype='NIFTI_GZ'),
reference='anat_skullstrip_orig_vol')
anat_skullstrip_orig_vol.in_file_a = anat
anat_skullstrip_orig_vol.in_file_b = anat_skullstrip.out_file
rp[R('T1w', desc='skullstrip-fsl',
suffix='mask')] = anat_skullstrip.mask_file
rp[R('T1w', desc='skullstrip-fsl',
suffix='brain')] = anat_skullstrip_orig_vol.out_file
def brain_extraction(wf, cfg, strat_pool, pipe_num, opt=None):
'''
{"name": "brain_extraction",
"config": "None",
"switch": "None",
"option_key": "None",
"option_val": "None",
"inputs": [(["desc-preproc_T1w", "desc-reorient_T1w", "T1w"],
["space-T1w_desc-brain_mask", "space-T1w_desc-acpcbrain_mask"])],
"outputs": ["desc-brain_T1w"]}
'''
'''
brain_mask_deoblique = pe.Node(interface=afni.Refit(),
name='brain_mask_deoblique')
brain_mask_deoblique.inputs.deoblique = True
wf.connect(inputnode, 'brain_mask',
brain_mask_deoblique, 'in_file')
brain_mask_reorient = pe.Node(interface=afni.Resample(),
name='brain_mask_reorient')
brain_mask_reorient.inputs.orientation = 'RPI'
brain_mask_reorient.inputs.outputtype = 'NIFTI_GZ'
wf.connect(brain_mask_deoblique, 'out_file',
brain_mask_reorient, 'in_file')
'''
anat_skullstrip_orig_vol = pe.Node(interface=afni.Calc(),
name=f'brain_extraction_{pipe_num}')
anat_skullstrip_orig_vol.inputs.expr = 'a*step(b)'
anat_skullstrip_orig_vol.inputs.outputtype = 'NIFTI_GZ'
node, out = strat_pool.get_data(
['desc-preproc_T1w', 'desc-reorient_T1w', 'T1w'])
wf.connect(node, out, anat_skullstrip_orig_vol, 'in_file_a')
node, out = strat_pool.get_data(
['space-T1w_desc-brain_mask', 'space-T1w_desc-acpcbrain_mask'])
wf.connect(node, out, anat_skullstrip_orig_vol, 'in_file_b')
outputs = {'desc-brain_T1w': (anat_skullstrip_orig_vol, 'out_file')}
return (wf, outputs)
def extract_label(path, label_id, output_name):
files2extract = glob.glob(path)
for subj in range(len(files2extract)):
print('extracting ', output_name, ' for subject ', subj)
subj_aparc = files2extract[subj]
mc = freesurfer.MRIConvert()
mc.inputs.in_file = subj_aparc
mc.inputs.out_file = os.path.join(
mc.inputs.in_file.split('.')[0] + mc.inputs.in_file.split('.')[1] +
'.nii.gz')
mc.run()
calc = afni.Calc()
calc.inputs.in_file_a = os.path.join(
mc.inputs.in_file.split('.')[0] + mc.inputs.in_file.split('.')[1] +
'.nii.gz')
calc.inputs.expr = 'amongst(a,' + str(label_id) + ')'
calc.inputs.out_file = os.path.join(
os.path.dirname(mc.inputs.in_file) + '/' + output_name + '.nii.gz')
calc.run()
def afni_wf(name='AFNISkullStripWorkflow'):
"""
Skull-stripping workflow
Derived from the codebase of the QAP:
https://github.com/preprocessed-connectomes-project/\
quality-assessment-protocol/blob/master/qap/anatomical_preproc.py#L105
"""
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['in_file']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['bias_corrected', 'out_file', 'out_mask', 'bias_image']),
name='outputnode')
inu_n4 = pe.Node(ants.N4BiasFieldCorrection(dimension=3, save_bias=True),
name='CorrectINU')
sstrip = pe.Node(afni.SkullStrip(outputtype='NIFTI_GZ'), name='skullstrip')
sstrip_orig_vol = pe.Node(afni.Calc(expr='a*step(b)',
outputtype='NIFTI_GZ'),
name='sstrip_orig_vol')
binarize = pe.Node(fsl.Threshold(args='-bin', thresh=1.e-3),
name='binarize')
workflow.connect([(inputnode, sstrip_orig_vol, [('in_file', 'in_file_a')]),
(inputnode, inu_n4, [('in_file', 'input_image')]),
(inu_n4, sstrip, [('output_image', 'in_file')]),
(sstrip, sstrip_orig_vol, [('out_file', 'in_file_b')]),
(sstrip_orig_vol, binarize, [('out_file', 'in_file')]),
(sstrip_orig_vol, outputnode, [('out_file', 'out_file')
]),
(binarize, outputnode, [('out_file', 'out_mask')]),
(inu_n4, outputnode, [('output_image', 'bias_corrected'),
('bias_image', 'bias_image')])])
return workflow
def test_calc():
input_map = dict(
args=dict(argstr='%s', ),
environ=dict(usedefault=True, ),
expr=dict(
argstr='-expr %s',
mandatory=True,
),
ignore_exception=dict(usedefault=True, ),
in_file_a=dict(
argstr='-a %s',
mandatory=True,
),
in_file_b=dict(argstr=' -b %s', ),
out_file=dict(argstr='-prefix %s', ),
single_idx=dict(),
start_idx=dict(requires=['stop_idx'], ),
stop_idx=dict(requires=['start_idx'], ),
)
instance = afni.Calc()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(instance.inputs.traits()[key],
metakey), value
def init_mask_finalize_wf(name="mask_finalize_wf"):
"""Creates a final mask using a combination of the t1 mask and dwi2mask
"""
inputnode = pe.Node(
niu.IdentityInterface(fields=['t1_mask', 'resampled_b0s']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=['mask_file']),
name='outputnode')
workflow = Workflow(name=name)
resample_t1_mask = pe.Node(afni.Resample(outputtype='NIFTI_GZ',
resample_mode="NN"),
name='resample_t1_mask')
b0mask = pe.Node(afni.Automask(outputtype='NIFTI_GZ'), name='b0mask')
or_mask = pe.Node(afni.Calc(outputtype='NIFTI_GZ', expr='step(a+b)'),
name='or_mask')
workflow.connect([(inputnode, resample_t1_mask, [('t1_mask', 'in_file'),
('resampled_b0s',
'master')]),
(inputnode, b0mask, [('resampled_b0s', 'in_file')]),
(b0mask, or_mask, [('out_file', 'in_file_a')]),
(resample_t1_mask, or_mask, [('out_file', 'in_file_b')]),
(or_mask, outputnode, [('out_file', 'mask_file')])])
return workflow
def connect_func_ingress(workflow,
strat_list,
c,
sub_dict,
subject_id,
input_creds_path,
unique_id=None):
for num_strat, strat in enumerate(strat_list):
if 'func' in sub_dict:
func_paths_dict = sub_dict['func']
else:
func_paths_dict = sub_dict['rest']
if unique_id is None:
workflow_name = f'func_gather_{num_strat}'
else:
workflow_name = f'func_gather_{unique_id}_{num_strat}'
func_wf = create_func_datasource(func_paths_dict, workflow_name)
func_wf.inputs.inputnode.set(subject=subject_id,
creds_path=input_creds_path,
dl_dir=c.workingDirectory)
func_wf.get_node('inputnode').iterables = \
("scan", list(func_paths_dict.keys()))
strat.update_resource_pool({
'subject': (func_wf, 'outputspec.subject'),
'scan': (func_wf, 'outputspec.scan')
})
# Grab field maps
diff = False
blip = False
fmap_rp_list = []
fmap_TE_list = []
if "fmap" in sub_dict:
for key in sub_dict["fmap"]:
gather_fmap = create_fmap_datasource(
sub_dict["fmap"], "fmap_gather_"
"{0}".format(key))
gather_fmap.inputs.inputnode.set(subject=subject_id,
creds_path=input_creds_path,
dl_dir=c.workingDirectory)
gather_fmap.inputs.inputnode.scan = key
strat.update_resource_pool({
key: (gather_fmap, 'outputspec.rest'),
"{0}_scan_params".format(key):
(gather_fmap, 'outputspec.scan_params')
})
fmap_rp_list.append(key)
if key == "diff_phase" or key == "diff_mag_one" or \
key == "diff_mag_two":
diff = True
get_fmap_metadata_imports = ['import json']
get_fmap_metadata = pe.Node(
Function(input_names=['data_config_scan_params'],
output_names=[
'echo_time', 'dwell_time', 'pe_direction'
],
function=get_fmap_phasediff_metadata,
imports=get_fmap_metadata_imports),
name='{0}_get_metadata_{1}'.format(key, num_strat))
node, out_file = strat["{}_scan_params".format(key)]
workflow.connect(node, out_file, get_fmap_metadata,
'data_config_scan_params')
strat.update_resource_pool({
"{}_TE".format(key): (get_fmap_metadata, 'echo_time'),
"{}_dwell".format(key):
(get_fmap_metadata, 'dwell_time'),
"{}_pedir".format(key):
(get_fmap_metadata, 'pe_direction')
})
fmap_TE_list.append("{}_TE".format(key))
if key == "epi_AP" or key == "epi_PA":
blip = True
if diff:
calc_delta_ratio = pe.Node(
Function(input_names=[
'dwell_time', 'echo_time_one', 'echo_time_two',
'echo_time_three'
],
output_names=['deltaTE', 'dwell_asym_ratio'],
function=calc_deltaTE_and_asym_ratio),
name='diff_distcor_calc_delta_{}'.format(num_strat))
node, out_file = strat['diff_phase_dwell']
workflow.connect(node, out_file, calc_delta_ratio,
'dwell_time')
node, out_file = strat[fmap_TE_list[0]]
workflow.connect(node, out_file, calc_delta_ratio,
'echo_time_one')
node, out_file = strat[fmap_TE_list[1]]
workflow.connect(node, out_file, calc_delta_ratio,
'echo_time_two')
if len(fmap_TE_list) > 2:
node, out_file = strat[fmap_TE_list[2]]
workflow.connect(node, out_file, calc_delta_ratio,
'echo_time_three')
strat.update_resource_pool({
'deltaTE': (calc_delta_ratio, 'deltaTE'),
'dwell_asym_ratio': (calc_delta_ratio, 'dwell_asym_ratio')
})
# Add in nodes to get parameters from configuration file
# a node which checks if scan_parameters are present for each scan
if unique_id is None:
workflow_name = f'scan_params_{num_strat}'
else:
workflow_name = f'scan_params_{unique_id}_{num_strat}'
scan_params = \
pe.Node(Function(
input_names=['data_config_scan_params',
'subject_id',
'scan',
'pipeconfig_tr',
'pipeconfig_tpattern',
'pipeconfig_start_indx',
'pipeconfig_stop_indx'],
output_names=['tr',
'tpattern',
'ref_slice',
'start_indx',
'stop_indx',
'pe_direction'],
function=get_scan_params,
as_module=True
), name=workflow_name)
if "Selected Functional Volume" in c.func_reg_input:
get_func_volume = pe.Node(
interface=afni.Calc(),
name='get_func_volume_{0}'.format(num_strat))
get_func_volume.inputs.set(expr='a',
single_idx=c.func_reg_input_volume,
outputtype='NIFTI_GZ')
workflow.connect(func_wf, 'outputspec.rest', get_func_volume,
'in_file_a')
# wire in the scan parameter workflow
workflow.connect(func_wf, 'outputspec.scan_params', scan_params,
'data_config_scan_params')
workflow.connect(func_wf, 'outputspec.subject', scan_params,
'subject_id')
workflow.connect(func_wf, 'outputspec.scan', scan_params, 'scan')
# connect in constants
scan_params.inputs.set(pipeconfig_start_indx=c.startIdx,
pipeconfig_stop_indx=c.stopIdx)
strat.update_resource_pool({
'raw_functional': (func_wf, 'outputspec.rest'),
'scan_id': (func_wf, 'outputspec.scan'),
'tr': (scan_params, 'tr'),
'tpattern': (scan_params, 'tpattern'),
'start_idx': (scan_params, 'start_indx'),
'stop_idx': (scan_params, 'stop_indx'),
'pe_direction': (scan_params, 'pe_direction'),
})
strat.set_leaf_properties(func_wf, 'outputspec.rest')
if "Selected Functional Volume" in c.func_reg_input:
strat.update_resource_pool(
{'selected_func_volume': (get_func_volume, 'out_file')})
return (workflow, diff, blip, fmap_rp_list)
def hmc_afni(name='fMRI_HMC_afni', st_correct=False, despike=False, deoblique=False):
"""A head motion correction (HMC) workflow for functional scans"""
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['in_file', 'fd_radius', 'start_idx', 'stop_idx']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['out_file', 'out_fd']), name='outputnode')
drop_trs = pe.Node(afni.Calc(expr='a', outputtype='NIFTI_GZ'),
name='drop_trs')
reorient = pe.Node(afni.Resample(
orientation='RPI', outputtype='NIFTI_GZ'), name='reorient')
get_mean_RPI = pe.Node(afni.TStat(
options='-mean', outputtype='NIFTI_GZ'), name='get_mean_RPI')
# calculate hmc parameters
hmc = pe.Node(
afni.Volreg(args='-Fourier -twopass', zpad=4, outputtype='NIFTI_GZ'),
name='motion_correct')
get_mean_motion = get_mean_RPI.clone('get_mean_motion')
hmc_A = hmc.clone('motion_correct_A')
hmc_A.inputs.md1d_file = 'max_displacement.1D'
# Compute the frame-wise displacement
calc_fd = pe.Node(niu.Function(
function=fd_jenkinson, input_names=['in_file', 'rmax'],
output_names=['out_fd']), name='calc_fd')
workflow.connect([
(inputnode, drop_trs, [('in_file', 'in_file_a'),
('start_idx', 'start_idx'),
('stop_idx', 'stop_idx')]),
(inputnode, calc_fd, [('fd_radius', 'rmax')]),
(reorient, get_mean_RPI, [('out_file', 'in_file')]),
(reorient, hmc, [('out_file', 'in_file')]),
(get_mean_RPI, hmc, [('out_file', 'basefile')]),
(hmc, get_mean_motion, [('out_file', 'in_file')]),
(reorient, hmc_A, [('out_file', 'in_file')]),
(get_mean_motion, hmc_A, [('out_file', 'basefile')]),
(hmc_A, outputnode, [('out_file', 'out_file')]),
(hmc_A, calc_fd, [('oned_matrix_save', 'in_file')]),
(calc_fd, outputnode, [('out_fd', 'out_fd')]),
])
# Slice timing correction, despiking, and deoblique
st_corr = pe.Node(afni.TShift(outputtype='NIFTI_GZ'), name='TimeShifts')
deoblique_node = pe.Node(afni.Refit(deoblique=True), name='deoblique')
despike_node = pe.Node(afni.Despike(outputtype='NIFTI_GZ'), name='despike')
if st_correct and despike and deoblique:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, despike_node, [('out_file', 'in_file')]),
(despike_node, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, reorient, [('out_file', 'in_file')])
])
elif st_correct and despike:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, despike_node, [('out_file', 'in_file')]),
(despike_node, reorient, [('out_file', 'in_file')]),
])
elif st_correct and deoblique:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, reorient, [('out_file', 'in_file')])
])
elif st_correct:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, reorient, [('out_file', 'in_file')])
])
elif despike and deoblique:
workflow.connect([
(drop_trs, despike_node, [('out_file', 'in_file')]),
(despike_node, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, reorient, [('out_file', 'in_file')])
])
elif despike:
workflow.connect([
(drop_trs, despike_node, [('out_file', 'in_file')]),
(despike_node, reorient, [('out_file', 'in_file')]),
])
elif deoblique:
workflow.connect([
(drop_trs, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, reorient, [('out_file', 'in_file')])
])
else:
workflow.connect([
(drop_trs, reorient, [('out_file', 'in_file')]),
])
return workflow
name='outputspec2')
inputnode2.inputs.drifter_result = results_path + '/' + data + '_1/drifter/drifter_corrected.nii.gz'
# Call fslcpgeom source dest, source is reorient output nii.gz file and dest is drifter folder nii.gz file
reoriented_file = results_path + '/' + data + '_1/reorient/corr_epi_reoriented.nii.gz'
drifted_file = results_path + '/' + data + '_1/drifter/drifter_corrected.nii.gz'
call(["fslcpgeom", reoriented_file, drifted_file])
# AFNI skullstrip and mean image skullstrip
tstat1 = pe.Node(interface=afni.TStat(args='-mean', outputtype="NIFTI_GZ"),
name='tstat1')
automask = pe.Node(interface=afni.Automask(dilate=1,
outputtype="NIFTI_GZ"),
name='automask')
skullstrip = pe.Node(interface=afni.Calc(expr='a*b',
outputtype="NIFTI_GZ"),
name='skullstrip')
tstat2 = pe.Node(interface=afni.TStat(args='-mean', outputtype="NIFTI_GZ"),
name='tstat2')
workflow2.connect(inputnode2, 'drifter_result', tstat1, 'in_file')
workflow2.connect(tstat1, 'out_file', automask, 'in_file')
workflow2.connect(automask, 'out_file', skullstrip, 'in_file_b')
workflow2.connect(inputnode2, 'drifter_result', skullstrip, 'in_file_a')
workflow2.connect(skullstrip, 'out_file', tstat2, 'in_file')
# Remove n (3) first volumes
trim = pe.Node(interface=Trim(begin_index=3), name='trim')
workflow2.connect(skullstrip, 'out_file', trim, 'in_file')
# Spatial smoothing, kernel sigma 2.00 mm (5 mm is too much)
def coregister_fmri_session(session_data,
t_r,
write_dir,
brain_volume,
use_rats_tool=True,
slice_timing=True,
prior_rigid_body_registration=False,
caching=False,
voxel_size_x=.1,
voxel_size_y=.1,
verbose=True,
**environ_kwargs):
"""
Coregistration of the subject's functional and anatomical images.
The functional volume is aligned to the anatomical, first with a rigid body
registration and then on a per-slice basis (only a fine correction, this is
mostly for correction of EPI distortion).
Parameters
----------
session_data : sammba.registration.SessionData
Single animal data, giving paths to its functional and anatomical
image, as well as it identifier.
t_r : float
Repetition time for the EPI, in seconds.
write_dir : str
Directory to save the output and temporary images.
brain_volume : int
Volume of the brain in mm3 used for brain extraction.
Typically 400 for mouse and 1800 for rat.
use_rats_tool : bool, optional
If True, brain mask is computed using RATS Mathematical Morphology.
Otherwise, a histogram-based brain segmentation is used.
prior_rigid_body_registration : bool, optional
If True, a rigid-body registration of the anat to the func is performed
prior to the warp. Useful if the images headers have missing/wrong
information.
voxel_size_x : float, optional
Resampling resolution for the x-axis, in mm.
voxel_size_y : float, optional
Resampling resolution for the y-axis, in mm.
caching : bool, optional
Wether or not to use caching.
verbose : bool, optional
If True, all steps are verbose. Note that caching implies some
verbosity in any case.
environ_kwargs : extra arguments keywords
Extra arguments keywords, passed to interfaces environ variable.
Returns
-------
the same sequence with each animal_data updated: the following attributes
are added
- `output_dir_` : str
Path to the output directory.
- `coreg_func_` : str
Path to paths to the coregistered functional image.
- `coreg_anat_` : str
Path to paths to the coregistered functional image.
- `coreg_transform_` : str
Path to the transform from anat to func.
Notes
-----
If `use_rats_tool` is turned on, RATS tool is used for brain extraction
and has to be cited. For more information, see
`RATS <http://www.iibi.uiowa.edu/content/rats-overview/>`_
"""
func_filename = session_data.func
anat_filename = session_data.anat
environ = {'AFNI_DECONFLICT': 'OVERWRITE'}
for (key, value) in environ_kwargs.items():
environ[key] = value
if verbose:
terminal_output = 'allatonce'
else:
terminal_output = 'none'
if use_rats_tool:
if segmentation.interfaces.Info().version() is None:
raise ValueError('Can not locate RATS')
else:
ComputeMask = segmentation.MathMorphoMask
else:
ComputeMask = segmentation.HistogramMask
if ants.base.Info().version is None:
raise ValueError('Can not locate ANTS')
if caching:
memory = Memory(write_dir)
tshift = memory.cache(afni.TShift)
clip_level = memory.cache(afni.ClipLevel)
volreg = memory.cache(afni.Volreg)
allineate = memory.cache(afni.Allineate)
tstat = memory.cache(afni.TStat)
compute_mask = memory.cache(ComputeMask)
calc = memory.cache(afni.Calc)
allineate = memory.cache(afni.Allineate)
allineate2 = memory.cache(afni.Allineate)
unifize = memory.cache(afni.Unifize)
bias_correct = memory.cache(ants.N4BiasFieldCorrection)
catmatvec = memory.cache(afni.CatMatvec)
warp = memory.cache(afni.Warp)
resample = memory.cache(afni.Resample)
slicer = memory.cache(afni.ZCutUp)
warp_apply = memory.cache(afni.NwarpApply)
qwarp = memory.cache(afni.Qwarp)
merge = memory.cache(afni.Zcat)
copy_geom = memory.cache(fsl.CopyGeom)
overwrite = False
for step in [
tshift, volreg, allineate, allineate2, tstat, compute_mask,
calc, unifize, resample, slicer, warp_apply, qwarp, merge
]:
step.interface().set_default_terminal_output(terminal_output)
else:
tshift = afni.TShift(terminal_output=terminal_output).run
clip_level = afni.ClipLevel().run
volreg = afni.Volreg(terminal_output=terminal_output).run
allineate = afni.Allineate(terminal_output=terminal_output).run
allineate2 = afni.Allineate(terminal_output=terminal_output
).run # TODO: remove after fixed bug
tstat = afni.TStat(terminal_output=terminal_output).run
compute_mask = ComputeMask().run
calc = afni.Calc(terminal_output=terminal_output).run
unifize = afni.Unifize(terminal_output=terminal_output).run
bias_correct = ants.N4BiasFieldCorrection(
terminal_output=terminal_output).run
catmatvec = afni.CatMatvec().run
warp = afni.Warp().run
resample = afni.Resample(terminal_output=terminal_output).run
slicer = afni.ZCutUp(terminal_output=terminal_output).run
warp_apply = afni.NwarpApply(terminal_output=terminal_output).run
qwarp = afni.Qwarp(terminal_output=terminal_output).run
merge = afni.Zcat(terminal_output=terminal_output).run
copy_geom = fsl.CopyGeom(terminal_output=terminal_output).run
overwrite = True
session_data._check_inputs()
output_dir = os.path.join(os.path.abspath(write_dir),
session_data.animal_id)
session_data._set_output_dir_(output_dir)
current_dir = os.getcwd()
os.chdir(output_dir)
output_files = []
#######################################
# Correct functional for slice timing #
#######################################
if slice_timing:
out_tshift = tshift(in_file=func_filename,
outputtype='NIFTI_GZ',
tpattern='altplus',
tr=str(t_r),
environ=environ)
func_filename = out_tshift.outputs.out_file
output_files.append(func_filename)
################################################
# Register functional volumes to the first one #
################################################
# XXX why do you need a thresholded image ?
out_clip_level = clip_level(in_file=func_filename)
out_calc_threshold = calc(in_file_a=func_filename,
expr='ispositive(a-{0}) * a'.format(
out_clip_level.outputs.clip_val),
outputtype='NIFTI_GZ')
thresholded_filename = out_calc_threshold.outputs.out_file
out_volreg = volreg( # XXX dfile not saved
in_file=thresholded_filename,
outputtype='NIFTI_GZ',
environ=environ,
oned_file=fname_presuffix(thresholded_filename,
suffix='Vr.1Dfile.1D',
use_ext=False),
oned_matrix_save=fname_presuffix(thresholded_filename,
suffix='Vr.aff12.1D',
use_ext=False))
# Apply the registration to the whole head
out_allineate = allineate(in_file=func_filename,
master=func_filename,
in_matrix=out_volreg.outputs.oned_matrix_save,
out_file=fname_presuffix(func_filename,
suffix='Av'),
environ=environ)
# 3dAllineate removes the obliquity. This is not a good way to readd it as
# removes motion correction info in the header if it were an AFNI file...as
# it happens it's NIfTI which does not store that so irrelevant!
out_copy_geom = copy_geom(dest_file=out_allineate.outputs.out_file,
in_file=out_volreg.outputs.out_file)
allineated_filename = out_copy_geom.outputs.out_file
# Create a (hopefully) nice mean image for use in the registration
out_tstat = tstat(in_file=allineated_filename,
args='-mean',
outputtype='NIFTI_GZ',
environ=environ)
# Update outputs
output_files.extend([
thresholded_filename, out_volreg.outputs.oned_matrix_save,
out_volreg.outputs.out_file, out_volreg.outputs.md1d_file,
allineated_filename, out_tstat.outputs.out_file
])
###########################################
# Corret anat and func for intensity bias #
###########################################
# Correct the functional average for intensities bias
out_bias_correct = bias_correct(input_image=out_tstat.outputs.out_file)
unbiased_func_filename = out_bias_correct.outputs.output_image
# Bias correct the antomical image
out_unifize = unifize(in_file=anat_filename,
outputtype='NIFTI_GZ',
environ=environ)
unbiased_anat_filename = out_unifize.outputs.out_file
# Update outputs
output_files.extend([unbiased_func_filename, unbiased_anat_filename])
#############################################
# Rigid-body registration anat -> mean func #
#############################################
if prior_rigid_body_registration:
# Mask the mean functional volume outside the brain.
out_clip_level = clip_level(in_file=unbiased_func_filename)
out_compute_mask_func = compute_mask(
in_file=unbiased_func_filename,
volume_threshold=brain_volume,
intensity_threshold=int(out_clip_level.outputs.clip_val))
out_cacl_func = calc(in_file_a=unbiased_func_filename,
in_file_b=out_compute_mask_func.outputs.out_file,
expr='a*b',
outputtype='NIFTI_GZ',
environ=environ)
# Mask the anatomical volume outside the brain.
out_clip_level = clip_level(in_file=unbiased_anat_filename)
out_compute_mask_anat = compute_mask(
in_file=unbiased_anat_filename,
volume_threshold=brain_volume,
intensity_threshold=int(out_clip_level.outputs.clip_val))
out_cacl_anat = calc(in_file_a=unbiased_anat_filename,
in_file_b=out_compute_mask_anat.outputs.out_file,
expr='a*b',
outputtype='NIFTI_GZ',
environ=environ)
# Compute the transformation from functional to anatomical brain
# XXX: why in this sense
out_allineate = allineate2(
in_file=out_cacl_func.outputs.out_file,
reference=out_cacl_anat.outputs.out_file,
out_matrix=fname_presuffix(out_cacl_func.outputs.out_file,
suffix='_shr.aff12.1D',
use_ext=False),
center_of_mass='',
warp_type='shift_rotate',
out_file=fname_presuffix(out_cacl_func.outputs.out_file,
suffix='_shr'),
environ=environ)
rigid_transform_file = out_allineate.outputs.out_matrix
output_files.extend([
out_compute_mask_func.outputs.out_file,
out_cacl_func.outputs.out_file,
out_compute_mask_anat.outputs.out_file,
out_cacl_anat.outputs.out_file, rigid_transform_file,
out_allineate.outputs.out_file
])
# apply the inverse transform to register the anatomical to the func
catmatvec_out_file = fname_presuffix(rigid_transform_file,
suffix='INV')
out_catmatvec = catmatvec(in_file=[(rigid_transform_file, 'I')],
oneline=True,
out_file=catmatvec_out_file)
output_files.append(out_catmatvec.outputs.out_file)
out_allineate = allineate(in_file=unbiased_anat_filename,
master=unbiased_func_filename,
in_matrix=out_catmatvec.outputs.out_file,
out_file=fname_presuffix(
unbiased_anat_filename,
suffix='_shr_in_func_space'),
environ=environ)
allineated_anat_filename = out_allineate.outputs.out_file
output_files.append(allineated_anat_filename)
else:
allineated_anat_filename = unbiased_anat_filename
############################################
# Nonlinear registration anat -> mean func #
############################################
# 3dWarp doesn't put the obliquity in the header, so do it manually
# This step generates one file per slice and per time point, so we are
# making sure they are removed at the end
out_warp = warp(in_file=allineated_anat_filename,
oblique_parent=unbiased_func_filename,
interp='quintic',
gridset=unbiased_func_filename,
outputtype='NIFTI_GZ',
verbose=True,
environ=environ)
registered_anat_filename = out_warp.outputs.out_file
registered_anat_oblique_filename = fix_obliquity(registered_anat_filename,
unbiased_func_filename,
verbose=verbose)
# Concatenate all the anat to func tranforms
mat_filename = fname_presuffix(registered_anat_filename,
suffix='_warp.mat',
use_ext=False)
# XXX Handle this correctly according to caching
if not os.path.isfile(mat_filename):
np.savetxt(mat_filename, [out_warp.runtime.stdout], fmt='%s')
output_files.append(mat_filename)
transform_filename = fname_presuffix(registered_anat_filename,
suffix='_anat_to_func.aff12.1D',
use_ext=False)
if prior_rigid_body_registration:
_ = catmatvec(in_file=[(mat_filename, 'ONELINE'),
(rigid_transform_file, 'ONELINE')],
oneline=True,
out_file=transform_filename)
else:
_ = catmatvec(in_file=[(mat_filename, 'ONELINE')],
oneline=True,
out_file=transform_filename)
##################################################
# Per-slice non-linear registration func -> anat #
##################################################
# Slice anatomical image
anat_img = nibabel.load(registered_anat_oblique_filename)
anat_n_slices = anat_img.header.get_data_shape()[2]
sliced_registered_anat_filenames = []
for slice_n in range(anat_n_slices):
out_slicer = slicer(in_file=registered_anat_oblique_filename,
keep='{0} {0}'.format(slice_n),
out_file=fname_presuffix(
registered_anat_oblique_filename,
suffix='Sl%d' % slice_n),
environ=environ)
oblique_slice = fix_obliquity(out_slicer.outputs.out_file,
registered_anat_oblique_filename,
verbose=verbose)
sliced_registered_anat_filenames.append(oblique_slice)
# Slice mean functional
sliced_bias_corrected_filenames = []
img = nibabel.load(func_filename)
n_slices = img.header.get_data_shape()[2]
for slice_n in range(n_slices):
out_slicer = slicer(in_file=unbiased_func_filename,
keep='{0} {0}'.format(slice_n),
out_file=fname_presuffix(unbiased_func_filename,
suffix='Sl%d' % slice_n),
environ=environ)
oblique_slice = fix_obliquity(out_slicer.outputs.out_file,
unbiased_func_filename,
verbose=verbose)
sliced_bias_corrected_filenames.append(oblique_slice)
# Below line is to deal with slices where there is no signal (for example
# rostral end of some anatomicals)
# The inverse warp frequently fails, Resampling can help it work better
# XXX why specifically .1 in voxel_size ?
voxel_size_z = anat_img.header.get_zooms()[2]
resampled_registered_anat_filenames = []
for sliced_registered_anat_filename in sliced_registered_anat_filenames:
out_resample = resample(in_file=sliced_registered_anat_filename,
voxel_size=(voxel_size_x, voxel_size_y,
voxel_size_z),
outputtype='NIFTI_GZ',
environ=environ)
resampled_registered_anat_filenames.append(
out_resample.outputs.out_file)
resampled_bias_corrected_filenames = []
for sliced_bias_corrected_filename in sliced_bias_corrected_filenames:
out_resample = resample(in_file=sliced_bias_corrected_filename,
voxel_size=(voxel_size_x, voxel_size_y,
voxel_size_z),
outputtype='NIFTI_GZ',
environ=environ)
resampled_bias_corrected_filenames.append(
out_resample.outputs.out_file)
# single slice non-linear functional to anatomical registration
warped_slices = []
warp_filenames = []
for (resampled_bias_corrected_filename,
resampled_registered_anat_filename) in zip(
resampled_bias_corrected_filenames,
resampled_registered_anat_filenames):
warped_slice = fname_presuffix(resampled_bias_corrected_filename,
suffix='_qw')
out_qwarp = qwarp(
in_file=resampled_bias_corrected_filename,
base_file=resampled_registered_anat_filename,
iwarp=True, # XXX: is this necessary
noneg=True,
blur=[0],
nmi=True,
noXdis=True,
allineate=True,
allineate_opts='-parfix 1 0 -parfix 2 0 -parfix 3 0 '
'-parfix 4 0 -parfix 5 0 -parfix 6 0 '
'-parfix 7 0 -parfix 9 0 '
'-parfix 10 0 -parfix 12 0',
out_file=warped_slice,
environ=environ)
warped_slices.append(out_qwarp.outputs.warped_source)
warp_filenames.append(out_qwarp.outputs.source_warp)
output_files.append(out_qwarp.outputs.base_warp)
# There are files geenrated by the allineate option
output_files.extend([
fname_presuffix(out_qwarp.outputs.warped_source, suffix='_Allin'),
fname_presuffix(out_qwarp.outputs.warped_source,
suffix='_Allin.nii',
use_ext=False),
fname_presuffix(out_qwarp.outputs.warped_source,
suffix='_Allin.aff12.1D',
use_ext=False)
])
# Resample the mean volume back to the initial resolution,
voxel_size = nibabel.load(unbiased_func_filename).header.get_zooms()
resampled_warped_slices = []
for warped_slice in warped_slices:
out_resample = resample(in_file=warped_slice,
voxel_size=voxel_size,
outputtype='NIFTI_GZ',
environ=environ)
resampled_warped_slices.append(out_resample.outputs.out_file)
# fix the obliquity
resampled_warped_slices_oblique = []
for (sliced_registered_anat_filename,
resampled_warped_slice) in zip(sliced_registered_anat_filenames,
resampled_warped_slices):
oblique_slice = fix_obliquity(resampled_warped_slice,
sliced_registered_anat_filename,
verbose=verbose)
resampled_warped_slices_oblique.append(oblique_slice)
# slice functional
sliced_func_filenames = []
for slice_n in range(n_slices):
out_slicer = slicer(in_file=allineated_filename,
keep='{0} {0}'.format(slice_n),
out_file=fname_presuffix(allineated_filename,
suffix='Sl%d' % slice_n),
environ=environ)
oblique_slice = fix_obliquity(out_slicer.outputs.out_file,
allineated_filename,
verbose=verbose)
sliced_func_filenames.append(oblique_slice)
# Apply the precomputed warp slice by slice
warped_func_slices = []
for (sliced_func_filename, warp_filename) in zip(sliced_func_filenames,
warp_filenames):
out_warp_apply = warp_apply(in_file=sliced_func_filename,
master=sliced_func_filename,
warp=warp_filename,
out_file=fname_presuffix(
sliced_func_filename, suffix='_qw'),
environ=environ)
warped_func_slices.append(out_warp_apply.outputs.out_file)
# Finally, merge all slices !
out_merge_func = merge(in_files=warped_func_slices,
outputtype='NIFTI_GZ',
environ=environ)
# Fix the obliquity
merged_oblique = fix_obliquity(out_merge_func.outputs.out_file,
allineated_filename,
verbose=verbose)
# Update the fmri data
setattr(session_data, "coreg_func_", merged_oblique)
setattr(session_data, "coreg_anat_", registered_anat_oblique_filename)
setattr(session_data, "coreg_transform_", transform_filename)
os.chdir(current_dir)
# Collect the outputs
output_files.extend(sliced_registered_anat_filenames +
sliced_bias_corrected_filenames +
resampled_registered_anat_filenames +
resampled_bias_corrected_filenames + warped_slices +
warp_filenames + resampled_warped_slices_oblique +
sliced_func_filenames + warped_func_slices)
if not caching:
for out_file in output_files:
if os.path.isfile(out_file):
os.remove(out_file)
def generate_summarize_tissue_mask(nuisance_wf,
pipeline_resource_pool,
regressor_descriptor,
regressor_selector,
use_ants=True,
ventricle_mask_exist=True):
"""
Add tissue mask generation into pipeline according to the selector.
:param nuisance_wf: Nuisance regressor workflow.
:param pipeline_resource_pool: dictionary of available resources.
:param regressor_descriptor: dictionary of steps to build, including keys:
'tissue', 'resolution', 'erosion'
:param regressor_selector: dictionary with the original selector
:return: the full path of the 3D nifti file containing the mask created by
this operation.
"""
steps = [
key for key in ['tissue', 'resolution', 'erosion']
if key in regressor_descriptor
]
full_mask_key = "_".join(regressor_descriptor[s] for s in steps)
for step_i, step in enumerate(steps):
mask_key = "_".join(regressor_descriptor[s]
for s in steps[:step_i + 1])
if mask_key in pipeline_resource_pool:
continue
node_mask_key = re.sub(r"[^\w]", "_", mask_key)
prev_mask_key = "_".join(regressor_descriptor[s]
for s in steps[:step_i])
if step == 'tissue':
pass
elif step == 'resolution':
mask_to_epi = pe.Node(interface=fsl.FLIRT(),
name='{}_flirt'.format(node_mask_key))
mask_to_epi.inputs.interp = 'nearestneighbour'
if regressor_selector['extraction_resolution'] == "Functional":
nuisance_wf.connect(
*(pipeline_resource_pool['Functional_mean'] +
(mask_to_epi, 'reference')))
else:
resolution = regressor_selector['extraction_resolution']
mask_to_epi.inputs.apply_isoxfm = resolution
nuisance_wf.connect(*(pipeline_resource_pool[
'Anatomical_{}mm'.format(resolution)] +
(mask_to_epi, 'reference')))
nuisance_wf.connect(*(pipeline_resource_pool[prev_mask_key] +
(mask_to_epi, 'in_file')))
pipeline_resource_pool[mask_key] = \
(mask_to_epi, 'out_file')
if full_mask_key.startswith('CerebrospinalFluid'):
pipeline_resource_pool = generate_summarize_tissue_mask_ventricles_masking(
nuisance_wf, pipeline_resource_pool, regressor_descriptor,
regressor_selector, node_mask_key, use_ants,
ventricle_mask_exist)
elif step == 'erosion':
erode_mask_node = pe.Node(afni.Calc(
args='-b a+i -c a-i -d a+j -e a-j -f a+k -g a-k',
expr='a*(1-amongst(0,b,c,d,e,f,g))',
outputtype='NIFTI_GZ'),
name='{}'.format(node_mask_key))
nuisance_wf.connect(*(pipeline_resource_pool[prev_mask_key] +
(erode_mask_node, 'in_file_a')))
pipeline_resource_pool[mask_key] = \
(erode_mask_node, 'out_file')
return pipeline_resource_pool, full_mask_key
def create_qc_carpet(wf_name='qc_carpet', output_image='qc_carpet'):
wf = pe.Workflow(name=wf_name)
input_node = pe.Node(util.IdentityInterface(fields=[
'functional_to_standard', 'mean_functional_to_standard',
'anatomical_gm_mask', 'anatomical_wm_mask', 'anatomical_csf_mask'
]),
name='inputspec')
output_node = pe.Node(util.IdentityInterface(fields=['carpet_plot']),
name='outputspec')
gm_resample = pe.Node(afni.Resample(), name='gm_resample')
gm_resample.inputs.outputtype = 'NIFTI'
wf.connect(input_node, 'anatomical_gm_mask', gm_resample, 'in_file')
wf.connect(input_node, 'mean_functional_to_standard', gm_resample,
'master')
gm_mask = pe.Node(afni.Calc(), name="gm_mask")
gm_mask.inputs.expr = 'astep(a, 0.5)'
gm_mask.inputs.outputtype = 'NIFTI'
wf.connect(gm_resample, 'out_file', gm_mask, 'in_file_a')
wm_resample = pe.Node(afni.Resample(), name='wm_resample')
wm_resample.inputs.outputtype = 'NIFTI'
wf.connect(input_node, 'anatomical_wm_mask', wm_resample, 'in_file')
wf.connect(input_node, 'mean_functional_to_standard', wm_resample,
'master')
wm_mask = pe.Node(afni.Calc(), name="wm_mask")
wm_mask.inputs.expr = 'astep(a, 0.5)'
wm_mask.inputs.outputtype = 'NIFTI'
wf.connect(wm_resample, 'out_file', wm_mask, 'in_file_a')
csf_resample = pe.Node(afni.Resample(), name='csf_resample')
csf_resample.inputs.outputtype = 'NIFTI'
wf.connect(input_node, 'anatomical_csf_mask', csf_resample, 'in_file')
wf.connect(input_node, 'mean_functional_to_standard', csf_resample,
'master')
csf_mask = pe.Node(afni.Calc(), name="csf_mask")
csf_mask.inputs.expr = 'astep(a, 0.5)'
csf_mask.inputs.outputtype = 'NIFTI'
wf.connect(csf_resample, 'out_file', csf_mask, 'in_file_a')
carpet_plot = pe.Node(Function(input_names=[
'gm_mask', 'wm_mask', 'csf_mask', 'functional_to_standard', 'output'
],
output_names=['carpet_plot'],
function=gen_carpet_plt,
as_module=True),
name='carpet_plot')
carpet_plot.inputs.output = output_image
wf.connect(gm_mask, 'out_file', carpet_plot, 'gm_mask')
wf.connect(wm_mask, 'out_file', carpet_plot, 'wm_mask')
wf.connect(csf_mask, 'out_file', carpet_plot, 'csf_mask')
wf.connect(input_node, 'functional_to_standard', carpet_plot,
'functional_to_standard')
wf.connect(carpet_plot, 'carpet_plot', output_node, 'carpet_plot')
return wf
def create_extract_pipe(params_template, params={}, name="extract_pipe"):
"""
Description: Extract T1 brain using AtlasBrex
Inputs:
inputnode:
restore_T1: preprocessed (debiased/denoised) T1 file name
restore_T1: preprocessed (debiased/denoised)T2 file name
arguments:
params_template: dictionary of info about template
params: dictionary of node sub-parameters (from a json file)
name: pipeline name (default = "extract_pipe")
Outputs:
smooth_mask.out_file:
Computed mask (after some smoothing)
"""
# creating pipeline
extract_pipe = pe.Workflow(name=name)
# creating inputnode
inputnode = pe.Node(
niu.IdentityInterface(fields=['restore_T1', 'restore_T2',
"indiv_params"]),
name='inputnode')
# atlas_brex
atlas_brex = NodeParams(AtlasBREX(),
params=parse_key(params, "atlas_brex"),
name='atlas_brex')
extract_pipe.connect(inputnode, "restore_T1",
atlas_brex, 't1_restored_file')
atlas_brex.inputs.NMT_file = params_template["template_head"]
atlas_brex.inputs.NMT_SS_file = params_template["template_brain"]
extract_pipe.connect(
inputnode, ("indiv_params", parse_key, "atlas_brex"),
atlas_brex, 'indiv_params')
# mask_brex
mask_brex = pe.Node(fsl.UnaryMaths(), name='mask_brex')
mask_brex.inputs.operation = 'bin'
extract_pipe.connect(atlas_brex, 'brain_file', mask_brex, 'in_file')
# smooth_mask
smooth_mask = pe.Node(fsl.UnaryMaths(), name='smooth_mask')
smooth_mask.inputs.operation = "bin"
smooth_mask.inputs.args = "-s 1 -thr 0.5 -bin"
extract_pipe.connect(mask_brex, 'out_file', smooth_mask, 'in_file')
# mult_T1
mult_T1 = pe.Node(afni.Calc(), name='mult_T1')
mult_T1.inputs.expr = "a*b"
mult_T1.inputs.outputtype = 'NIFTI_GZ'
extract_pipe.connect(inputnode, "restore_T1", mult_T1, 'in_file_a')
extract_pipe.connect(smooth_mask, 'out_file', mult_T1, 'in_file_b')
# mult_T2
mult_T2 = pe.Node(afni.Calc(), name='mult_T2')
mult_T2.inputs.expr = "a*b"
mult_T2.inputs.outputtype = 'NIFTI_GZ'
extract_pipe.connect(inputnode, 'restore_T2', mult_T2, 'in_file_a')
extract_pipe.connect(smooth_mask, 'out_file', mult_T2, 'in_file_b')
return extract_pipe
def afni_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
# Skull-stripping using AFNI 3dSkullStrip
inputnode_afni = pe.Node(util.IdentityInterface(fields=[
'mask_vol', 'shrink_factor', 'var_shrink_fac', 'shrink_fac_bot_lim',
'avoid_vent', 'niter', 'pushout', 'touchup', 'fill_hole', 'NN_smooth',
'smooth_final', 'avoid_eyes', 'use_edge', 'exp_frac', 'push_to_edge',
'use_skull', 'perc_int', 'max_inter_iter', 'blur_fwhm', 'fac', 'monkey'
]),
name=f'AFNI_options_{pipe_num}')
skullstrip_args = pe.Node(util.Function(
input_names=[
'spat_norm', 'spat_norm_dxyz', 'mask_vol', 'shrink_fac',
'var_shrink_fac', 'shrink_fac_bot_lim', 'avoid_vent', 'niter',
'pushout', 'touchup', 'fill_hole', 'NN_smooth', 'smooth_final',
'avoid_eyes', 'use_edge', 'exp_frac', 'push_to_edge', 'use_skull',
'perc_int', 'max_inter_iter', 'blur_fwhm', 'fac', 'monkey'
],
output_names=['expr'],
function=create_3dskullstrip_arg_string),
name=f'anat_skullstrip_args_{pipe_num}')
inputnode_afni.inputs.set(
mask_vol=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['mask_vol'],
shrink_factor=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['shrink_factor'],
var_shrink_fac=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['var_shrink_fac'],
shrink_fac_bot_lim=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['shrink_factor_bot_lim'],
avoid_vent=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['avoid_vent'],
niter=cfg.anatomical_preproc['brain_extraction']['AFNI-3dSkullStrip']
['n_iterations'],
pushout=cfg.anatomical_preproc['brain_extraction']['AFNI-3dSkullStrip']
['pushout'],
touchup=cfg.anatomical_preproc['brain_extraction']['AFNI-3dSkullStrip']
['touchup'],
fill_hole=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['fill_hole'],
NN_smooth=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['NN_smooth'],
smooth_final=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['smooth_final'],
avoid_eyes=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['avoid_eyes'],
use_edge=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['use_edge'],
exp_frac=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['exp_frac'],
push_to_edge=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['push_to_edge'],
use_skull=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['use_skull'],
perc_int=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['perc_int'],
max_inter_iter=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['max_inter_iter'],
fac=cfg.anatomical_preproc['brain_extraction']['AFNI-3dSkullStrip']
['fac'],
blur_fwhm=cfg.anatomical_preproc['brain_extraction']
['AFNI-3dSkullStrip']['blur_fwhm'],
monkey=cfg.anatomical_preproc['brain_extraction']['AFNI-3dSkullStrip']
['monkey'],
)
wf.connect([(inputnode_afni, skullstrip_args,
[('mask_vol', 'mask_vol'), ('shrink_factor', 'shrink_fac'),
('var_shrink_fac', 'var_shrink_fac'),
('shrink_fac_bot_lim', 'shrink_fac_bot_lim'),
('avoid_vent', 'avoid_vent'), ('niter', 'niter'),
('pushout', 'pushout'), ('touchup', 'touchup'),
('fill_hole', 'fill_hole'), ('avoid_eyes', 'avoid_eyes'),
('use_edge', 'use_edge'), ('exp_frac', 'exp_frac'),
('NN_smooth', 'NN_smooth'), ('smooth_final', 'smooth_final'),
('push_to_edge', 'push_to_edge'), ('use_skull', 'use_skull'),
('perc_int', 'perc_int'),
('max_inter_iter', 'max_inter_iter'),
('blur_fwhm', 'blur_fwhm'), ('fac', 'fac'),
('monkey', 'monkey')])])
anat_skullstrip = pe.Node(interface=afni.SkullStrip(),
name=f'anat_skullstrip_{pipe_num}')
anat_skullstrip.inputs.outputtype = 'NIFTI_GZ'
node, out = strat_pool.get_data(
['desc-preproc_T1w', 'desc-reorient_T1w', 'T1w'])
wf.connect(node, out, anat_skullstrip, 'in_file')
wf.connect(skullstrip_args, 'expr', anat_skullstrip, 'args')
# Generate anatomical brain mask
anat_brain_mask = pe.Node(interface=afni.Calc(),
name=f'anat_brain_mask_{pipe_num}')
anat_brain_mask.inputs.expr = 'step(a)'
anat_brain_mask.inputs.outputtype = 'NIFTI_GZ'
wf.connect(anat_skullstrip, 'out_file', anat_brain_mask, 'in_file_a')
outputs = {'space-T1w_desc-brain_mask': (anat_brain_mask, 'out_file')}
return (wf, outputs)
def _create_split_hemi_pipe(params, params_template, name="split_hemi_pipe"):
"""Description: Split segmentated tissus according hemisheres after \
removal of cortical structure
Processing steps:
- TODO
Params:
- None so far
Inputs:
inputnode:
warpinv_file:
non-linear transformation (from NMT_subject_align)
inv_transfo_file:
inverse transformation
aff_file:
affine transformation file
t1_ref_file:
preprocessd T1
segmented_file:
from atropos segmentation, with all the tissues segmented
arguments:
params:
dictionary of node sub-parameters (from a json file)
name:
pipeline name (default = "split_hemi_pipe")
Outputs:
"""
split_hemi_pipe = pe.Workflow(name=name)
# creating inputnode
inputnode = pe.Node(niu.IdentityInterface(fields=[
'warpinv_file', 'inv_transfo_file', 'aff_file', 't1_ref_file',
'segmented_file'
]),
name='inputnode')
# get values
if "cereb_template" in params_template.keys():
cereb_template_file = params_template["cereb_template"]
# ### cereb
# Binarize cerebellum
bin_cereb = pe.Node(interface=fsl.UnaryMaths(), name='bin_cereb')
bin_cereb.inputs.operation = "bin"
bin_cereb.inputs.in_file = cereb_template_file
# Warp cereb brainmask to subject space
warp_cereb = pe.Node(interface=reg.NwarpApplyPriors(),
name='warp_cereb')
warp_cereb.inputs.in_file = cereb_template_file
warp_cereb.inputs.out_file = cereb_template_file
warp_cereb.inputs.interp = "NN"
warp_cereb.inputs.args = "-overwrite"
split_hemi_pipe.connect(bin_cereb, 'out_file', warp_cereb, 'in_file')
split_hemi_pipe.connect(inputnode, 'aff_file', warp_cereb, 'master')
split_hemi_pipe.connect(inputnode, 'warpinv_file', warp_cereb, "warp")
# Align cereb template
align_cereb = pe.Node(interface=afni.Allineate(), name='align_cereb')
align_cereb.inputs.final_interpolation = "nearestneighbour"
align_cereb.inputs.overwrite = True
align_cereb.inputs.outputtype = "NIFTI_GZ"
split_hemi_pipe.connect(warp_cereb, 'out_file', align_cereb,
"in_file") # -source
split_hemi_pipe.connect(inputnode, 't1_ref_file', align_cereb,
"reference") # -base
split_hemi_pipe.connect(inputnode, 'inv_transfo_file', align_cereb,
"in_matrix") # -1Dmatrix_apply
if "L_hemi_template" in params_template.keys() and \
"R_hemi_template" in params_template.keys():
L_hemi_template_file = params_template["L_hemi_template"]
R_hemi_template_file = params_template["R_hemi_template"]
# Warp L hemi template brainmask to subject space
warp_L_hemi = pe.Node(interface=reg.NwarpApplyPriors(),
name='warp_L_hemi')
warp_L_hemi.inputs.in_file = L_hemi_template_file
warp_L_hemi.inputs.out_file = L_hemi_template_file
warp_L_hemi.inputs.interp = "NN"
warp_L_hemi.inputs.args = "-overwrite"
split_hemi_pipe.connect(inputnode, 'aff_file', warp_L_hemi, 'master')
split_hemi_pipe.connect(inputnode, 'warpinv_file', warp_L_hemi, "warp")
# Align L hemi template
align_L_hemi = pe.Node(interface=afni.Allineate(), name='align_L_hemi')
align_L_hemi.inputs.final_interpolation = "nearestneighbour"
align_L_hemi.inputs.overwrite = True
align_L_hemi.inputs.outputtype = "NIFTI_GZ"
split_hemi_pipe.connect(warp_L_hemi, 'out_file', align_L_hemi,
"in_file") # -source
split_hemi_pipe.connect(inputnode, 't1_ref_file', align_L_hemi,
"reference") # -base
split_hemi_pipe.connect(inputnode, 'inv_transfo_file', align_L_hemi,
"in_matrix") # -1Dmatrix_apply
# Warp R hemi template brainmask to subject space
warp_R_hemi = pe.Node(interface=reg.NwarpApplyPriors(),
name='warp_R_hemi')
warp_R_hemi.inputs.in_file = R_hemi_template_file
warp_R_hemi.inputs.out_file = R_hemi_template_file
warp_R_hemi.inputs.interp = "NN"
warp_R_hemi.inputs.args = "-overwrite"
split_hemi_pipe.connect(inputnode, 'aff_file', warp_R_hemi, 'master')
split_hemi_pipe.connect(inputnode, 'warpinv_file', warp_R_hemi, "warp")
# Align R hemi template
align_R_hemi = pe.Node(interface=afni.Allineate(), name='align_R_hemi')
align_R_hemi.inputs.final_interpolation = "nearestneighbour"
align_R_hemi.inputs.overwrite = True
align_R_hemi.inputs.outputtype = "NIFTI_GZ"
split_hemi_pipe.connect(warp_R_hemi, 'out_file', align_R_hemi,
"in_file") # -source
split_hemi_pipe.connect(inputnode, 't1_ref_file', align_R_hemi,
"reference") # -base
split_hemi_pipe.connect(inputnode, 'inv_transfo_file', align_R_hemi,
"in_matrix") # -1Dmatrix_apply
elif "LR_hemi_template" in params_template.keys():
LR_hemi_template_file = params_template["LR_hemi_template"]
# Warp LR hemi template brainmask to subject space
warp_LR_hemi = pe.Node(interface=reg.NwarpApplyPriors(),
name='warp_LR_hemi')
warp_LR_hemi.inputs.in_file = LR_hemi_template_file
warp_LR_hemi.inputs.out_file = LR_hemi_template_file
warp_LR_hemi.inputs.interp = "NN"
warp_LR_hemi.inputs.args = "-overwrite"
split_hemi_pipe.connect(inputnode, 'aff_file', warp_LR_hemi, 'master')
split_hemi_pipe.connect(inputnode, 'warpinv_file', warp_LR_hemi,
"warp")
# Align LR hemi template
align_LR_hemi = pe.Node(interface=afni.Allineate(),
name='align_LR_hemi')
align_LR_hemi.inputs.final_interpolation = "nearestneighbour"
align_LR_hemi.inputs.overwrite = True
align_LR_hemi.inputs.outputtype = "NIFTI_GZ"
split_hemi_pipe.connect(warp_LR_hemi, 'out_file', align_LR_hemi,
"in_file") # -source
split_hemi_pipe.connect(inputnode, 't1_ref_file', align_LR_hemi,
"reference") # -base
split_hemi_pipe.connect(inputnode, 'inv_transfo_file', align_LR_hemi,
"in_matrix") # -1Dmatrix_apply
split_LR = pe.Node(interface=niu.Function(
input_names=["LR_mask_file"],
output_names=["L_mask_file", "R_mask_file"],
function=split_LR_mask),
name="split_LR")
split_hemi_pipe.connect(align_LR_hemi, "out_file", split_LR,
'LR_mask_file')
else:
print("Error, could not find LR_hemi_template or L_hemi_template and \
R_hemi_template, skipping")
print(params_template.keys())
exit()
# Using LH and RH masks to obtain hemisphere segmentation masks
calc_L_hemi = pe.Node(interface=afni.Calc(), name='calc_L_hemi')
calc_L_hemi.inputs.expr = 'a*b/b'
calc_L_hemi.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(inputnode, 'segmented_file', calc_L_hemi,
"in_file_a")
if "LR_hemi_template" in params_template.keys():
split_hemi_pipe.connect(split_LR, 'L_mask_file', calc_L_hemi,
"in_file_b")
else:
split_hemi_pipe.connect(align_L_hemi, 'out_file', calc_L_hemi,
"in_file_b")
# R_hemi
calc_R_hemi = pe.Node(interface=afni.Calc(), name='calc_R_hemi')
calc_R_hemi.inputs.expr = 'a*b/b'
calc_R_hemi.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(inputnode, 'segmented_file', calc_R_hemi,
"in_file_a")
if "LR_hemi_template" in params_template.keys():
split_hemi_pipe.connect(split_LR, 'R_mask_file', calc_R_hemi,
"in_file_b")
else:
split_hemi_pipe.connect(align_R_hemi, 'out_file', calc_R_hemi,
"in_file_b")
# remove cerebellum from left and right brain segmentations
calc_nocb_L_hemi = pe.Node(interface=afni.Calc(), name='calc_nocb_L_hemi')
calc_nocb_L_hemi.inputs.expr = '(a*(not (b)))'
calc_nocb_L_hemi.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(calc_L_hemi, 'out_file', calc_nocb_L_hemi,
"in_file_a")
split_hemi_pipe.connect(align_cereb, 'out_file', calc_nocb_L_hemi,
"in_file_b")
calc_nocb_R_hemi = pe.Node(interface=afni.Calc(), name='calc_nocb_R_hemi')
calc_nocb_R_hemi.inputs.expr = '(a*(not (b)))'
calc_nocb_R_hemi.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(calc_R_hemi, 'out_file', calc_nocb_R_hemi,
"in_file_a")
split_hemi_pipe.connect(align_cereb, 'out_file', calc_nocb_R_hemi,
"in_file_b")
# create L/R GM and WM no-cerebellum masks from subject brain segmentation
calc_GM_nocb_L_hemi = pe.Node(interface=afni.Calc(),
name='calc_GM_nocb_L_hemi')
calc_GM_nocb_L_hemi.inputs.expr = 'iszero(a-2)'
calc_GM_nocb_L_hemi.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(calc_nocb_L_hemi, 'out_file', calc_GM_nocb_L_hemi,
"in_file_a")
calc_WM_nocb_L_hemi = pe.Node(interface=afni.Calc(),
name='calc_WM_nocb_L_hemi')
calc_WM_nocb_L_hemi.inputs.expr = 'iszero(a-3)'
calc_WM_nocb_L_hemi.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(calc_nocb_L_hemi, 'out_file', calc_WM_nocb_L_hemi,
"in_file_a")
calc_GM_nocb_R_hemi = pe.Node(interface=afni.Calc(),
name='calc_GM_nocb_R_hemi')
calc_GM_nocb_R_hemi.inputs.expr = 'iszero(a-2)'
calc_GM_nocb_R_hemi.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(calc_nocb_R_hemi, 'out_file', calc_GM_nocb_R_hemi,
"in_file_a")
calc_WM_nocb_R_hemi = pe.Node(interface=afni.Calc(),
name='calc_WM_nocb_R_hemi')
calc_WM_nocb_R_hemi.inputs.expr = 'iszero(a-3)'
calc_WM_nocb_R_hemi.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(calc_nocb_R_hemi, 'out_file', calc_WM_nocb_R_hemi,
"in_file_a")
# Extract Cerebellum using template mask transformed to subject space
extract_cereb = pe.Node(interface=afni.Calc(), name='extract_cereb')
extract_cereb.inputs.expr = 'a*b/b'
extract_cereb.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(inputnode, 't1_ref_file', extract_cereb,
"in_file_a")
split_hemi_pipe.connect(align_cereb, 'out_file', extract_cereb,
"in_file_b")
# Extract L.GM using template mask transformed to subject space
extract_L_GM = pe.Node(interface=afni.Calc(), name='extract_L_GM')
extract_L_GM.inputs.expr = 'a*b/b'
extract_L_GM.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(inputnode, 't1_ref_file', extract_L_GM,
"in_file_a")
split_hemi_pipe.connect(calc_GM_nocb_L_hemi, 'out_file', extract_L_GM,
"in_file_b")
# Extract L.WM using template mask transformed to subject space
extract_L_WM = pe.Node(interface=afni.Calc(), name='extract_L_WM')
extract_L_WM.inputs.expr = 'a*b/b'
extract_L_WM.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(inputnode, 't1_ref_file', extract_L_WM,
"in_file_a")
split_hemi_pipe.connect(calc_WM_nocb_L_hemi, 'out_file', extract_L_WM,
"in_file_b")
# Extract L.GM using template mask transformed to subject space
extract_R_GM = pe.Node(interface=afni.Calc(), name='extract_R_GM')
extract_R_GM.inputs.expr = 'a*b/b'
extract_R_GM.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(inputnode, 't1_ref_file', extract_R_GM,
"in_file_a")
split_hemi_pipe.connect(calc_GM_nocb_R_hemi, 'out_file', extract_R_GM,
"in_file_b")
# Extract L.WM using template mask transformed to subject space
extract_R_WM = pe.Node(interface=afni.Calc(), name='extract_R_WM')
extract_R_WM.inputs.expr = 'a*b/b'
extract_R_WM.inputs.outputtype = 'NIFTI_GZ'
split_hemi_pipe.connect(inputnode, 't1_ref_file', extract_R_WM,
"in_file_a")
split_hemi_pipe.connect(calc_WM_nocb_R_hemi, 'out_file', extract_R_WM,
"in_file_b")
return split_hemi_pipe
def main(args=None):
args = arg_parser().parse_args(args)
FLAIR = args.FLAIR
MPRAGE = args.T1
prefix=args.prefix + '.'
if args.mask is None:
args.temp_mask = os.path.abspath (args.temp_mask)
args.brain_template = os.path.abspath(args.brain_template)
args.temp_prob = os.path.abspath(args.temp_prob)
if not os.path.isfile(args.temp_mask):
raise Exception("template mask not foud")
if not os.path.isfile(args.brain_template):
raise Exception("brain template mask not foud")
if not os.path.isfile(args.temp_prob):
raise Exception("template probability mask not foud")
elif not os.path.isfile(args.mask):
raise Exception("T1 mask file not foud")
if not os.path.isfile(MPRAGE):
raise Exception("Input T1 file not found")
if not os.path.isfile(FLAIR):
raise Exception("Input FLAIR file not found")
if args.outfolder is not None:
abs_out = os.path.abspath(args.outfolder)
#print(abs_out)
if not os.path.exists(abs_out):
#if selecting a new folder copy the files (not sure how to specify different folder under nipype when it runs sh scripts from ants)
os.mkdir(abs_out)
copyfile(os.path.abspath(MPRAGE),os.path.join(abs_out,os.path.basename(MPRAGE)))
copyfile(os.path.abspath(FLAIR),os.path.join(abs_out,os.path.basename(FLAIR)))
if args.mask is not None:
if os.path.isfile(args.mask):
copyfile(os.path.abspath(args.mask),os.path.join(abs_out, prefix + 'MPRAGE.mask.nii.gz'))
os.chdir(args.outfolder)
elif args.mask is not None:
copyfile(os.path.abspath(args.mask),os.path.join(os.path.abspath(args.mask), prefix + 'MPRAGE.mask.nii.gz'))
if args.mask is None:
# T1 brain extraction
brainextraction = BrainExtraction()
brainextraction.inputs.dimension = 3
brainextraction.inputs.anatomical_image = MPRAGE
brainextraction.inputs.brain_template = args.brain_template
brainextraction.inputs.brain_probability_mask = args.temp_prob
brainextraction.inputs.extraction_registration_mask= args.temp_mask
brainextraction.inputs.debug=True
print("brain extraction")
print(' ')
print(brainextraction.cmdline)
print('-'*30)
brainextraction.run()
os.rename('highres001_BrainExtractionMask.nii.gz',prefix +'MPRAGE.mask.nii.gz')
os.rename('highres001_BrainExtractionBrain.nii.gz',prefix +'MPRAGE.brain.nii.gz')
os.remove('highres001_BrainExtractionPrior0GenericAffine.mat')
os.rmdir('highres001_')
#two step registration with ants (step1)
reg = Registration()
reg.inputs.fixed_image = FLAIR
reg.inputs.moving_image = MPRAGE
reg.inputs.output_transform_prefix = "output_"
reg.inputs.output_warped_image = prefix + 'output_warped_image.nii.gz'
reg.inputs.dimension = 3
reg.inputs.transforms = ['Rigid']
reg.inputs.transform_parameters = [[0.1]]
reg.inputs.radius_or_number_of_bins = [32]
reg.inputs.metric = ['MI']
reg.inputs.sampling_percentage = [0.1]
reg.inputs.sampling_strategy = ['Regular']
reg.inputs.shrink_factors = [[4,3,2,1]]
reg.inputs.smoothing_sigmas = [[3,2,1,0]]
reg.inputs.sigma_units = ['vox']
reg.inputs.use_histogram_matching = [False]
reg.inputs.number_of_iterations = [[1000,500,250,100]]
reg.inputs.winsorize_lower_quantile = 0.025
reg.inputs.winsorize_upper_quantile = 0.975
print("first pass registration")
print(' ')
print(reg.cmdline)
print('-'*30)
reg.run()
os.rename('output_0GenericAffine.mat',prefix + 'MPRAGE_to_FLAIR.firstpass.mat')
#apply tranform MPRAGE mask to FLAIR
at = ApplyTransforms()
at.inputs.dimension = 3
at.inputs.input_image = prefix + 'MPRAGE.mask.nii.gz'
at.inputs.reference_image = FLAIR
at.inputs.output_image = prefix + 'FLAIR.mask.nii.gz'
at.inputs.interpolation = 'MultiLabel'
at.inputs.default_value = 0
at.inputs.transforms = [ prefix + 'MPRAGE_to_FLAIR.firstpass.mat']
at.inputs.invert_transform_flags = [False]
print("apply stranform to T1 maks")
print(' ')
print(at.cmdline)
print('-'*30)
at.run()
# bias correct FLAIR and MPRAGE
n4m = N4BiasFieldCorrection()
n4m.inputs.dimension = 3
n4m.inputs.input_image = MPRAGE
n4m.inputs.mask_image = prefix + 'MPRAGE.mask.nii.gz'
n4m.inputs.bspline_fitting_distance = 300
n4m.inputs.shrink_factor = 3
n4m.inputs.n_iterations = [50,50,30,20]
n4m.inputs.output_image = prefix + 'MPRAGE.N4.nii.gz'
print("bias correcting T1")
print(' ')
print(n4m.cmdline)
print('-'*30)
n4m.run()
n4f = copy.deepcopy(n4m)
n4f.inputs.input_image = FLAIR
n4f.inputs.mask_image = prefix + 'FLAIR.mask.nii.gz'
n4f.inputs.output_image = prefix + 'FLAIR.N4.nii.gz'
print("bias correcting FLAIR")
print(' ')
print(n4f.cmdline)
print('-'*30)
n4f.run()
# mask bias corrected FLAIR and MPRAGE
calc = afni.Calc()
calc.inputs.in_file_a = prefix + 'FLAIR.N4.nii.gz'
calc.inputs.in_file_b = prefix + 'FLAIR.mask.nii.gz'
calc.inputs.expr='a*b'
calc.inputs.out_file = prefix + 'FLAIR.N4.masked.nii.gz'
calc.inputs.outputtype = 'NIFTI'
calc.inputs.overwrite = True
calc.run()
calc1= copy.deepcopy(calc)
calc1.inputs.in_file_a = prefix + 'MPRAGE.N4.nii.gz'
calc1.inputs.in_file_b = prefix + 'MPRAGE.mask.nii.gz'
calc1.inputs.out_file = prefix + 'MPRAGE.N4.masked.nii.gz'
calc1.inputs.overwrite = True
calc1.run()
#register bias corrected
reg1 = copy.deepcopy(reg)
reg1.inputs.output_transform_prefix = "output_"
reg1.inputs.output_warped_image = prefix + 'output_warped_image.nii.gz'
reg1.inputs.initial_moving_transform = prefix +'MPRAGE_to_FLAIR.firstpass.mat'
print("second pass registration")
print(' ')
print(reg1.cmdline)
print('-'*30)
reg1.run()
os.rename('output_0GenericAffine.mat',prefix +'MPRAGE_to_FLAIR.secondpass.mat')
#generate final mask in FLAIR space
atf = ApplyTransforms()
atf.inputs.dimension = 3
atf.inputs.input_image = prefix + 'MPRAGE.N4.nii.gz'
atf.inputs.reference_image = FLAIR
atf.inputs.output_image = prefix + 'MPRAGE.N4.toFLAIR.nii.gz'
atf.inputs.interpolation = 'BSpline'
atf.inputs.interpolation_parameters = (3,)
atf.inputs.default_value = 0
atf.inputs.transforms = [prefix + 'MPRAGE_to_FLAIR.secondpass.mat']
atf.inputs.invert_transform_flags = [False]
print("final apply transform")
print(' ')
print(atf.cmdline)
print('-'*30)
atf.run()
#cleanup
os.remove(prefix + 'output_warped_image.nii.gz')
if args.outfolder is not None:
os.remove(os.path.join(abs_out,os.path.basename(MPRAGE)))
os.remove(os.path.join(abs_out,os.path.basename(FLAIR)))
if args.mask is None:
os.remove(prefix + 'MPRAGE.brain.nii.gz')
if not args.storetemp:
os.remove(prefix + 'MPRAGE.mask.nii.gz')
os.remove(prefix + 'MPRAGE_to_FLAIR.firstpass.mat')
os.remove(prefix + 'FLAIR.N4.masked.nii.gz')
os.remove(prefix + 'MPRAGE.N4.masked.nii.gz')
os.remove(prefix + 'MPRAGE.N4.nii.gz')
return
def hmc_afni(settings, name='fMRI_HMC_afni', st_correct=False, despike=False,
deoblique=False, start_idx=None, stop_idx=None):
"""
A :abbr:`HMC (head motion correction)` workflow for
functional scans
.. workflow::
from mriqc.workflows.functional import hmc_afni
wf = hmc_afni({'biggest_file_size_gb': 1})
"""
biggest_file_gb = settings.get("biggest_file_size_gb", 1)
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['in_file', 'fd_radius', 'start_idx', 'stop_idx']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['out_file', 'out_fd']), name='outputnode')
if (start_idx is not None) or (stop_idx is not None):
drop_trs = pe.Node(afni.Calc(expr='a', outputtype='NIFTI_GZ'),
name='drop_trs')
workflow.connect([
(inputnode, drop_trs, [('in_file', 'in_file_a'),
('start_idx', 'start_idx'),
('stop_idx', 'stop_idx')]),
])
else:
drop_trs = pe.Node(niu.IdentityInterface(fields=['out_file']),
name='drop_trs')
workflow.connect([
(inputnode, drop_trs, [('in_file', 'out_file')]),
])
gen_ref = pe.Node(nwr.EstimateReferenceImage(mc_method="AFNI"), name="gen_ref")
# calculate hmc parameters
hmc = pe.Node(
afni.Volreg(args='-Fourier -twopass', zpad=4, outputtype='NIFTI_GZ'),
name='motion_correct', mem_gb=biggest_file_gb * 2.5)
# Compute the frame-wise displacement
fdnode = pe.Node(nac.FramewiseDisplacement(normalize=False,
parameter_source="AFNI"),
name='ComputeFD')
workflow.connect([
(inputnode, fdnode, [('fd_radius', 'radius')]),
(gen_ref, hmc, [('ref_image', 'basefile')]),
(hmc, outputnode, [('out_file', 'out_file')]),
(hmc, fdnode, [('oned_file', 'in_file')]),
(fdnode, outputnode, [('out_file', 'out_fd')]),
])
# Slice timing correction, despiking, and deoblique
st_corr = pe.Node(afni.TShift(outputtype='NIFTI_GZ'), name='TimeShifts')
deoblique_node = pe.Node(afni.Refit(deoblique=True), name='deoblique')
despike_node = pe.Node(afni.Despike(outputtype='NIFTI_GZ'), name='despike')
if st_correct and despike and deoblique:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, despike_node, [('out_file', 'in_file')]),
(despike_node, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
elif st_correct and despike:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, despike_node, [('out_file', 'in_file')]),
(despike_node, gen_ref, [('out_file', 'in_file')]),
(despike_node, hmc, [('out_file', 'in_file')]),
])
elif st_correct and deoblique:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
elif st_correct:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, gen_ref, [('out_file', 'in_file')]),
(st_corr, hmc, [('out_file', 'in_file')]),
])
elif despike and deoblique:
workflow.connect([
(drop_trs, despike_node, [('out_file', 'in_file')]),
(despike_node, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
elif despike:
workflow.connect([
(drop_trs, despike_node, [('out_file', 'in_file')]),
(despike_node, gen_ref, [('out_file', 'in_file')]),
(despike_node, hmc, [('out_file', 'in_file')]),
])
elif deoblique:
workflow.connect([
(drop_trs, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
else:
workflow.connect([
(drop_trs, gen_ref, [('out_file', 'in_file')]),
(drop_trs, hmc, [('out_file', 'in_file')]),
])
return workflow
def temporal_variance_mask(threshold, by_slice=False, erosion=False, degree=1):
threshold_method = "VAR"
if isinstance(threshold, str):
regex_match = {
"SD": r"([0-9]+(\.[0-9]+)?)\s*SD",
"PCT": r"([0-9]+(\.[0-9]+)?)\s*PCT",
}
for method, regex in regex_match.items():
matched = re.match(regex, threshold)
if matched:
threshold_method = method
threshold_value = matched.groups()[0]
try:
threshold_value = float(threshold_value)
except:
raise ValueError(
"Error converting threshold value {0} from {1} to a "
"floating point number. The threshold value can "
"contain SD or PCT for selecting a threshold based on "
"the variance distribution, otherwise it should be a "
"floating point number.".format(threshold_value, threshold))
if threshold_value < 0:
raise ValueError(
"Threshold value should be positive, instead of {0}.".format(
threshold_value))
if threshold_method is "PCT" and threshold_value >= 100.0:
raise ValueError(
"Percentile should be less than 100, received {0}.".format(
threshold_value))
threshold = threshold_value
wf = pe.Workflow(name='tcompcor')
input_node = pe.Node(util.IdentityInterface(
fields=['functional_file_path', 'mask_file_path']),
name='inputspec')
output_node = pe.Node(util.IdentityInterface(fields=['mask']),
name='outputspec')
# C-PAC default performs linear regression while nipype performs quadratic regression
detrend = pe.Node(afni.Detrend(args='-polort {0}'.format(degree),
outputtype='NIFTI'),
name='detrend')
wf.connect(input_node, 'functional_file_path', detrend, 'in_file')
std = pe.Node(afni.TStat(args='-nzstdev', outputtype='NIFTI'), name='std')
wf.connect(input_node, 'mask_file_path', std, 'mask')
wf.connect(detrend, 'out_file', std, 'in_file')
var = pe.Node(afni.Calc(expr='a*a', outputtype='NIFTI'), name='var')
wf.connect(std, 'out_file', var, 'in_file_a')
if by_slice:
slices = pe.Node(fsl.Slice(), name='slicer')
wf.connect(var, 'out_file', slices, 'in_file')
mask_slices = pe.Node(fsl.Slice(), name='mask_slicer')
wf.connect(input_node, 'mask_file_path', mask_slices, 'in_file')
mapper = pe.MapNode(
util.IdentityInterface(fields=['out_file', 'mask_file']),
name='slice_mapper',
iterfield=['out_file', 'mask_file'])
wf.connect(slices, 'out_files', mapper, 'out_file')
wf.connect(mask_slices, 'out_files', mapper, 'mask_file')
else:
mapper_list = pe.Node(util.Merge(1), name='slice_mapper_list')
wf.connect(var, 'out_file', mapper_list, 'in1')
mask_mapper_list = pe.Node(util.Merge(1),
name='slice_mask_mapper_list')
wf.connect(input_node, 'mask_file_path', mask_mapper_list, 'in1')
mapper = pe.Node(
util.IdentityInterface(fields=['out_file', 'mask_file']),
name='slice_mapper')
wf.connect(mapper_list, 'out', mapper, 'out_file')
wf.connect(mask_mapper_list, 'out', mapper, 'mask_file')
if threshold_method is "PCT":
threshold_node = pe.MapNode(Function(
input_names=['in_file', 'mask', 'threshold_pct'],
output_names=['threshold'],
function=compute_pct_threshold,
as_module=True),
name='threshold_value',
iterfield=['in_file', 'mask'])
threshold_node.inputs.threshold_pct = threshold_value
wf.connect(mapper, 'out_file', threshold_node, 'in_file')
wf.connect(mapper, 'mask_file', threshold_node, 'mask')
elif threshold_method is "SD":
threshold_node = pe.MapNode(Function(
input_names=['in_file', 'mask', 'threshold_sd'],
output_names=['threshold'],
function=compute_sd_threshold,
as_module=True),
name='threshold_value',
iterfield=['in_file', 'mask'])
threshold_node.inputs.threshold_sd = threshold_value
wf.connect(mapper, 'out_file', threshold_node, 'in_file')
wf.connect(mapper, 'mask_file', threshold_node, 'mask')
else:
threshold_node = pe.MapNode(Function(
input_names=['in_file', 'mask', 'threshold'],
output_names=['threshold'],
function=compute_threshold,
as_module=True),
name='threshold_value',
iterfield=['in_file', 'mask'])
threshold_node.inputs.threshold = threshold_value
wf.connect(mapper, 'out_file', threshold_node, 'in_file')
wf.connect(mapper, 'mask_file', threshold_node, 'mask')
threshold_mask = pe.MapNode(interface=fsl.maths.Threshold(),
name='threshold',
iterfield=['in_file', 'thresh'])
threshold_mask.inputs.args = '-bin'
wf.connect(mapper, 'out_file', threshold_mask, 'in_file')
wf.connect(threshold_node, 'threshold', threshold_mask, 'thresh')
merge_slice_masks = pe.Node(interface=fsl.Merge(),
name='merge_slice_masks')
merge_slice_masks.inputs.dimension = 'z'
wf.connect(threshold_mask, 'out_file', merge_slice_masks, 'in_files')
wf.connect(merge_slice_masks, 'merged_file', output_node, 'mask')
return wf
def create_anat_preproc(template_path=None,
mask_path=None,
regmask_path=None,
method='afni',
already_skullstripped=False,
non_local_means_filtering=True,
n4_correction=True,
wf_name='anat_preproc'):
"""
The main purpose of this workflow is to process T1 scans. Raw mprage file is deobliqued, reoriented
into RPI and skullstripped. Also, a whole brain only mask is generated from the skull stripped image
for later use in registration.
Returns
-------
anat_preproc : workflow
Anatomical Preprocessing Workflow
Notes
-----
`Source <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/anat_preproc/anat_preproc.py>`_
Workflow Inputs::
inputspec.anat : string
User input anatomical (T1) Image, in any of the 8 orientations
Workflow Outputs::
outputspec.refit : string
Path to deobliqued anatomical image
outputspec.reorient : string
Path to RPI oriented anatomical image
outputspec.skullstrip : string
Path to skull stripped RPI oriented mprage file with normalized intensities.
outputspec.brain : string
Path to skull stripped RPI brain image with original intensity values and not normalized or scaled.
Order of commands:
- Deobliqing the scans. ::
3drefit -deoblique mprage.nii.gz
- Re-orienting the Image into Right-to-Left Posterior-to-Anterior Inferior-to-Superior (RPI) orientation ::
3dresample -orient RPI
-prefix mprage_RPI.nii.gz
-inset mprage.nii.gz
- Skull-Stripping the image ::
Using AFNI ::
3dSkullStrip -input mprage_RPI.nii.gz
-o_ply mprage_RPI_3dT.nii.gz
or using BET ::
bet mprage_RPI.nii.gz
- The skull-stripping step modifies the intensity values. To get back the original intensity values, we do an element wise product of RPI data with step function of skull-stripped data ::
3dcalc -a mprage_RPI.nii.gz
-b mprage_RPI_3dT.nii.gz
-expr 'a*step(b)'
-prefix mprage_RPI_3dc.nii.gz
High Level Workflow Graph:
.. image:: ../images/anatpreproc_graph.dot.png
:width: 500
Detailed Workflow Graph:
.. image:: ../images/anatpreproc_graph_detailed.dot.png
:width: 500
Examples
--------
>>> from CPAC.anat_preproc import create_anat_preproc
>>> preproc = create_anat_preproc()
>>> preproc.inputs.inputspec.anat = 'sub1/anat/mprage.nii.gz'
>>> preproc.run() #doctest: +SKIP
"""
preproc = pe.Workflow(name=wf_name)
inputnode = pe.Node(util.IdentityInterface(fields=['anat', 'brain_mask']),
name='inputspec')
outputnode = pe.Node(util.IdentityInterface(
fields=['refit', 'reorient', 'skullstrip', 'brain', 'brain_mask']),
name='outputspec')
anat_deoblique = pe.Node(interface=afni.Refit(), name='anat_deoblique')
anat_deoblique.inputs.deoblique = True
preproc.connect(inputnode, 'anat', anat_deoblique, 'in_file')
preproc.connect(anat_deoblique, 'out_file', outputnode, 'refit')
# Disable non_local_means_filtering and n4_correction when run niworkflows-ants
if method == 'niworkflows-ants':
non_local_means_filtering = False
n4_correction = False
if non_local_means_filtering and n4_correction:
denoise = pe.Node(interface=ants.DenoiseImage(), name='anat_denoise')
preproc.connect(anat_deoblique, 'out_file', denoise, 'input_image')
n4 = pe.Node(interface=ants.N4BiasFieldCorrection(dimension=3,
shrink_factor=2,
copy_header=True),
name='anat_n4')
preproc.connect(denoise, 'output_image', n4, 'input_image')
elif non_local_means_filtering and not n4_correction:
denoise = pe.Node(interface=ants.DenoiseImage(), name='anat_denoise')
preproc.connect(anat_deoblique, 'out_file', denoise, 'input_image')
elif not non_local_means_filtering and n4_correction:
n4 = pe.Node(interface=ants.N4BiasFieldCorrection(dimension=3,
shrink_factor=2,
copy_header=True),
name='anat_n4')
preproc.connect(anat_deoblique, 'out_file', n4, 'input_image')
# Anatomical reorientation
anat_reorient = pe.Node(interface=afni.Resample(), name='anat_reorient')
anat_reorient.inputs.orientation = 'RPI'
anat_reorient.inputs.outputtype = 'NIFTI_GZ'
if n4_correction:
preproc.connect(n4, 'output_image', anat_reorient, 'in_file')
elif non_local_means_filtering and not n4_correction:
preproc.connect(denoise, 'output_image', anat_reorient, 'in_file')
else:
preproc.connect(anat_deoblique, 'out_file', anat_reorient, 'in_file')
preproc.connect(anat_reorient, 'out_file', outputnode, 'reorient')
if already_skullstripped:
anat_skullstrip = pe.Node(
interface=util.IdentityInterface(fields=['out_file']),
name='anat_skullstrip')
preproc.connect(anat_reorient, 'out_file', anat_skullstrip, 'out_file')
preproc.connect(anat_skullstrip, 'out_file', outputnode, 'skullstrip')
preproc.connect(anat_skullstrip, 'out_file', outputnode, 'brain')
else:
if method == 'afni':
# Skull-stripping using AFNI 3dSkullStrip
inputnode_afni = pe.Node(util.IdentityInterface(fields=[
'shrink_factor', 'var_shrink_fac', 'shrink_fac_bot_lim',
'avoid_vent', 'niter', 'pushout', 'touchup', 'fill_hole',
'avoid_eyes', 'use_edge', 'exp_frac', 'smooth_final',
'push_to_edge', 'use_skull', 'perc_int', 'max_inter_iter',
'blur_fwhm', 'fac', 'monkey'
]),
name='AFNI_options')
skullstrip_args = pe.Node(util.Function(
input_names=[
'spat_norm', 'spat_norm_dxyz', 'shrink_fac',
'var_shrink_fac', 'shrink_fac_bot_lim', 'avoid_vent',
'niter', 'pushout', 'touchup', 'fill_hole', 'avoid_eyes',
'use_edge', 'exp_frac', 'smooth_final', 'push_to_edge',
'use_skull', 'perc_int', 'max_inter_iter', 'blur_fwhm',
'fac', 'monkey'
],
output_names=['expr'],
function=create_3dskullstrip_arg_string),
name='anat_skullstrip_args')
preproc.connect([(inputnode_afni, skullstrip_args,
[('shrink_factor', 'shrink_fac'),
('var_shrink_fac', 'var_shrink_fac'),
('shrink_fac_bot_lim', 'shrink_fac_bot_lim'),
('avoid_vent', 'avoid_vent'),
('niter', 'niter'), ('pushout', 'pushout'),
('touchup', 'touchup'),
('fill_hole', 'fill_hole'),
('avoid_eyes', 'avoid_eyes'),
('use_edge', 'use_edge'),
('exp_frac', 'exp_frac'),
('smooth_final', 'smooth_final'),
('push_to_edge', 'push_to_edge'),
('use_skull', 'use_skull'),
('perc_int', 'perc_int'),
('max_inter_iter', 'max_inter_iter'),
('blur_fwhm', 'blur_fwhm'), ('fac', 'fac'),
('monkey', 'monkey')])])
anat_skullstrip = pe.Node(interface=afni.SkullStrip(),
name='anat_skullstrip')
anat_skullstrip.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_reorient, 'out_file', anat_skullstrip,
'in_file')
preproc.connect(skullstrip_args, 'expr', anat_skullstrip, 'args')
preproc.connect(anat_skullstrip, 'out_file', outputnode,
'skullstrip')
# Apply skull-stripping step mask to original volume
anat_skullstrip_orig_vol = pe.Node(interface=afni.Calc(),
name='anat_skullstrip_orig_vol')
anat_skullstrip_orig_vol.inputs.expr = 'a*step(b)'
anat_skullstrip_orig_vol.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_reorient, 'out_file',
anat_skullstrip_orig_vol, 'in_file_a')
anat_brain_mask = pe.Node(interface=afni.Calc(),
name='anat_brain_mask')
anat_brain_mask.inputs.expr = 'step(a)'
anat_brain_mask.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_skullstrip, 'out_file', anat_brain_mask,
'in_file_a')
preproc.connect(anat_skullstrip, 'out_file',
anat_skullstrip_orig_vol, 'in_file_b')
preproc.connect(anat_brain_mask, 'out_file', outputnode,
'brain_mask')
preproc.connect(anat_skullstrip_orig_vol, 'out_file', outputnode,
'brain')
elif method == 'fsl':
# Skull-stripping using FSL BET
inputnode_bet = pe.Node(util.IdentityInterface(fields=[
'frac', 'mask_boolean', 'mesh_boolean', 'outline', 'padding',
'radius', 'reduce_bias', 'remove_eyes', 'robust', 'skull',
'surfaces', 'threshold', 'vertical_gradient'
]),
name='BET_options')
anat_skullstrip = pe.Node(interface=fsl.BET(),
name='anat_skullstrip')
preproc.connect(anat_reorient, 'out_file', anat_skullstrip,
'in_file')
preproc.connect([(inputnode_bet, anat_skullstrip, [
('frac', 'frac'),
('mask_boolean', 'mask'),
('mesh_boolean', 'mesh'),
('outline', 'outline'),
('padding', 'padding'),
('radius', 'radius'),
('reduce_bias', 'reduce_bias'),
('remove_eyes', 'remove_eyes'),
('robust', 'robust'),
('skull', 'skull'),
('surfaces', 'surfaces'),
('threshold', 'threshold'),
('vertical_gradient', 'vertical_gradient'),
])])
preproc.connect(anat_skullstrip, 'out_file', outputnode,
'skullstrip')
# Apply skull-stripping step mask to original volume
anat_skullstrip_orig_vol = pe.Node(interface=afni.Calc(),
name='anat_skullstrip_orig_vol')
anat_skullstrip_orig_vol.inputs.expr = 'a*step(b)'
anat_skullstrip_orig_vol.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_reorient, 'out_file',
anat_skullstrip_orig_vol, 'in_file_a')
preproc.connect(anat_skullstrip, 'out_file',
anat_skullstrip_orig_vol, 'in_file_b')
preproc.connect(anat_skullstrip, 'mask_file', outputnode,
'brain_mask')
preproc.connect(anat_skullstrip_orig_vol, 'out_file', outputnode,
'brain')
elif method == 'niworkflows-ants':
# Skull-stripping using niworkflows-ants
anat_skullstrip_ants = init_brain_extraction_wf(
tpl_target_path=template_path,
tpl_mask_path=mask_path,
tpl_regmask_path=regmask_path,
name='anat_skullstrip_ants')
preproc.connect(anat_reorient, 'out_file', anat_skullstrip_ants,
'inputnode.in_files')
preproc.connect(anat_skullstrip_ants, 'copy_xform.out_file',
outputnode, 'skullstrip')
preproc.connect(anat_skullstrip_ants, 'copy_xform.out_file',
outputnode, 'brain')
preproc.connect(anat_skullstrip_ants,
'atropos_wf.copy_xform.out_mask', outputnode,
'brain_mask')
elif method == 'mask':
anat_skullstrip_orig_vol = pe.Node(interface=afni.Calc(),
name='anat_skullstrip_orig_vol')
anat_skullstrip_orig_vol.inputs.expr = 'a*step(b)'
anat_skullstrip_orig_vol.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_reorient, 'out_file',
anat_skullstrip_orig_vol, 'in_file_a')
preproc.connect(inputnode, 'brain_mask', anat_skullstrip_orig_vol,
'in_file_b')
preproc.connect(inputnode, 'brain_mask', outputnode, 'brain_mask')
preproc.connect(anat_skullstrip_orig_vol, 'out_file', outputnode,
'brain')
return preproc
def create_anat_preproc(method='afni',
already_skullstripped=False,
c=None,
wf_name='anat_preproc'):
"""The main purpose of this workflow is to process T1 scans. Raw mprage file is deobliqued, reoriented
into RPI and skullstripped. Also, a whole brain only mask is generated from the skull stripped image
for later use in registration.
Returns
-------
anat_preproc : workflow
Anatomical Preprocessing Workflow
Notes
-----
`Source <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/anat_preproc/anat_preproc.py>`_
Workflow Inputs::
inputspec.anat : string
User input anatomical (T1) Image, in any of the 8 orientations
Workflow Outputs::
outputspec.refit : string
Path to deobliqued anatomical image
outputspec.reorient : string
Path to RPI oriented anatomical image
outputspec.skullstrip : string
Path to skull stripped RPI oriented mprage file with normalized intensities.
outputspec.brain : string
Path to skull stripped RPI brain image with original intensity values and not normalized or scaled.
Order of commands:
- Deobliqing the scans. ::
3drefit -deoblique mprage.nii.gz
- Re-orienting the Image into Right-to-Left Posterior-to-Anterior Inferior-to-Superior (RPI) orientation ::
3dresample -orient RPI
-prefix mprage_RPI.nii.gz
-inset mprage.nii.gz
- Skull-Stripping the image ::
Using AFNI ::
3dSkullStrip -input mprage_RPI.nii.gz
-o_ply mprage_RPI_3dT.nii.gz
or using BET ::
bet mprage_RPI.nii.gz
- The skull-stripping step modifies the intensity values. To get back the original intensity values, we do an element wise product of RPI data with step function of skull-stripped data ::
3dcalc -a mprage_RPI.nii.gz
-b mprage_RPI_3dT.nii.gz
-expr 'a*step(b)'
-prefix mprage_RPI_3dc.nii.gz
High Level Workflow Graph:
.. image:: ../images/anatpreproc_graph.dot.png
:width: 500
Detailed Workflow Graph:
.. image:: ../images/anatpreproc_graph_detailed.dot.png
:width: 500
Examples
--------
>>> from CPAC.anat_preproc import create_anat_preproc
>>> preproc = create_anat_preproc()
>>> preproc.inputs.inputspec.anat = 'sub1/anat/mprage.nii.gz'
>>> preproc.run() #doctest: +SKIP
"""
preproc = pe.Workflow(name=wf_name)
inputnode = pe.Node(util.IdentityInterface(fields=['anat', 'brain_mask']),
name='inputspec')
outputnode = pe.Node(util.IdentityInterface(
fields=['refit', 'reorient', 'skullstrip', 'brain', 'brain_mask']),
name='outputspec')
anat_deoblique = pe.Node(interface=afni.Refit(), name='anat_deoblique')
anat_deoblique.inputs.deoblique = True
preproc.connect(inputnode, 'anat', anat_deoblique, 'in_file')
preproc.connect(anat_deoblique, 'out_file', outputnode, 'refit')
# Disable non_local_means_filtering and n4_bias_field_correction when run niworkflows-ants
if method == 'niworkflows-ants':
c.non_local_means_filtering = False
c.n4_bias_field_correction = False
if c.non_local_means_filtering and c.n4_bias_field_correction:
denoise = pe.Node(interface=ants.DenoiseImage(), name='anat_denoise')
preproc.connect(anat_deoblique, 'out_file', denoise, 'input_image')
n4 = pe.Node(interface=ants.N4BiasFieldCorrection(dimension=3,
shrink_factor=2,
copy_header=True),
name='anat_n4')
preproc.connect(denoise, 'output_image', n4, 'input_image')
elif c.non_local_means_filtering and not c.n4_bias_field_correction:
denoise = pe.Node(interface=ants.DenoiseImage(), name='anat_denoise')
preproc.connect(anat_deoblique, 'out_file', denoise, 'input_image')
elif not c.non_local_means_filtering and c.n4_bias_field_correction:
n4 = pe.Node(interface=ants.N4BiasFieldCorrection(dimension=3,
shrink_factor=2,
copy_header=True),
name='anat_n4')
preproc.connect(anat_deoblique, 'out_file', n4, 'input_image')
# Anatomical reorientation
anat_reorient = pe.Node(interface=afni.Resample(), name='anat_reorient')
anat_reorient.inputs.orientation = 'RPI'
anat_reorient.inputs.outputtype = 'NIFTI_GZ'
if c.n4_bias_field_correction:
preproc.connect(n4, 'output_image', anat_reorient, 'in_file')
elif c.non_local_means_filtering and not c.n4_bias_field_correction:
preproc.connect(denoise, 'output_image', anat_reorient, 'in_file')
else:
preproc.connect(anat_deoblique, 'out_file', anat_reorient, 'in_file')
preproc.connect(anat_reorient, 'out_file', outputnode, 'reorient')
if already_skullstripped:
anat_skullstrip = pe.Node(
interface=util.IdentityInterface(fields=['out_file']),
name='anat_skullstrip')
preproc.connect(anat_reorient, 'out_file', anat_skullstrip, 'out_file')
preproc.connect(anat_skullstrip, 'out_file', outputnode, 'skullstrip')
preproc.connect(anat_skullstrip, 'out_file', outputnode, 'brain')
else:
if method == 'afni':
# Skull-stripping using AFNI 3dSkullStrip
inputnode_afni = pe.Node(util.IdentityInterface(fields=[
'mask_vol', 'shrink_factor', 'var_shrink_fac',
'shrink_fac_bot_lim', 'avoid_vent', 'niter', 'pushout',
'touchup', 'fill_hole', 'avoid_eyes', 'use_edge', 'exp_frac',
'smooth_final', 'push_to_edge', 'use_skull', 'perc_int',
'max_inter_iter', 'blur_fwhm', 'fac', 'monkey'
]),
name='AFNI_options')
skullstrip_args = pe.Node(util.Function(
input_names=[
'spat_norm', 'spat_norm_dxyz', 'mask_vol', 'shrink_fac',
'var_shrink_fac', 'shrink_fac_bot_lim', 'avoid_vent',
'niter', 'pushout', 'touchup', 'fill_hole', 'avoid_eyes',
'use_edge', 'exp_frac', 'smooth_final', 'push_to_edge',
'use_skull', 'perc_int', 'max_inter_iter', 'blur_fwhm',
'fac', 'monkey'
],
output_names=['expr'],
function=create_3dskullstrip_arg_string),
name='anat_skullstrip_args')
preproc.connect([(inputnode_afni, skullstrip_args,
[('mask_vol', 'mask_vol'),
('shrink_factor', 'shrink_fac'),
('var_shrink_fac', 'var_shrink_fac'),
('shrink_fac_bot_lim', 'shrink_fac_bot_lim'),
('avoid_vent', 'avoid_vent'),
('niter', 'niter'), ('pushout', 'pushout'),
('touchup', 'touchup'),
('fill_hole', 'fill_hole'),
('avoid_eyes', 'avoid_eyes'),
('use_edge', 'use_edge'),
('exp_frac', 'exp_frac'),
('smooth_final', 'smooth_final'),
('push_to_edge', 'push_to_edge'),
('use_skull', 'use_skull'),
('perc_int', 'perc_int'),
('max_inter_iter', 'max_inter_iter'),
('blur_fwhm', 'blur_fwhm'), ('fac', 'fac'),
('monkey', 'monkey')])])
anat_skullstrip = pe.Node(interface=afni.SkullStrip(),
name='anat_skullstrip')
anat_skullstrip.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_reorient, 'out_file', anat_skullstrip,
'in_file')
preproc.connect(skullstrip_args, 'expr', anat_skullstrip, 'args')
# Generate anatomical brain mask
anat_brain_mask = pe.Node(interface=afni.Calc(),
name='anat_brain_mask')
anat_brain_mask.inputs.expr = 'step(a)'
anat_brain_mask.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_skullstrip, 'out_file', anat_brain_mask,
'in_file_a')
# Apply skull-stripping step mask to original volume
anat_skullstrip_orig_vol = pe.Node(interface=afni.Calc(),
name='anat_skullstrip_orig_vol')
anat_skullstrip_orig_vol.inputs.expr = 'a*step(b)'
anat_skullstrip_orig_vol.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_reorient, 'out_file',
anat_skullstrip_orig_vol, 'in_file_a')
preproc.connect(anat_brain_mask, 'out_file',
anat_skullstrip_orig_vol, 'in_file_b')
preproc.connect(anat_brain_mask, 'out_file', outputnode,
'brain_mask')
preproc.connect(anat_skullstrip_orig_vol, 'out_file', outputnode,
'brain')
elif method == 'fsl':
# Skull-stripping using FSL BET
inputnode_bet = pe.Node(util.IdentityInterface(fields=[
'frac', 'mask_boolean', 'mesh_boolean', 'outline', 'padding',
'radius', 'reduce_bias', 'remove_eyes', 'robust', 'skull',
'surfaces', 'threshold', 'vertical_gradient'
]),
name='BET_options')
anat_skullstrip = pe.Node(interface=fsl.BET(),
name='anat_skullstrip')
anat_skullstrip.inputs.output_type = 'NIFTI_GZ'
preproc.connect(anat_reorient, 'out_file', anat_skullstrip,
'in_file')
preproc.connect([(inputnode_bet, anat_skullstrip, [
('frac', 'frac'),
('mask_boolean', 'mask'),
('mesh_boolean', 'mesh'),
('outline', 'outline'),
('padding', 'padding'),
('radius', 'radius'),
('reduce_bias', 'reduce_bias'),
('remove_eyes', 'remove_eyes'),
('robust', 'robust'),
('skull', 'skull'),
('surfaces', 'surfaces'),
('threshold', 'threshold'),
('vertical_gradient', 'vertical_gradient'),
])])
preproc.connect(anat_skullstrip, 'out_file', outputnode,
'skullstrip')
# Apply skull-stripping step mask to original volume
anat_skullstrip_orig_vol = pe.Node(interface=afni.Calc(),
name='anat_skullstrip_orig_vol')
anat_skullstrip_orig_vol.inputs.expr = 'a*step(b)'
anat_skullstrip_orig_vol.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_reorient, 'out_file',
anat_skullstrip_orig_vol, 'in_file_a')
preproc.connect(anat_skullstrip, 'out_file',
anat_skullstrip_orig_vol, 'in_file_b')
preproc.connect(anat_skullstrip, 'mask_file', outputnode,
'brain_mask')
preproc.connect(anat_skullstrip_orig_vol, 'out_file', outputnode,
'brain')
elif method == 'niworkflows-ants':
# Skull-stripping using niworkflows-ants
anat_skullstrip_ants = init_brain_extraction_wf(
tpl_target_path=c.niworkflows_ants_template_path,
tpl_mask_path=c.niworkflows_ants_mask_path,
tpl_regmask_path=c.niworkflows_ants_regmask_path,
name='anat_skullstrip_ants')
preproc.connect(anat_reorient, 'out_file', anat_skullstrip_ants,
'inputnode.in_files')
preproc.connect(anat_skullstrip_ants, 'copy_xform.out_file',
outputnode, 'skullstrip')
preproc.connect(anat_skullstrip_ants, 'copy_xform.out_file',
outputnode, 'brain')
preproc.connect(anat_skullstrip_ants,
'atropos_wf.copy_xform.out_mask', outputnode,
'brain_mask')
elif method == 'mask':
brain_mask_deoblique = pe.Node(interface=afni.Refit(),
name='brain_mask_deoblique')
brain_mask_deoblique.inputs.deoblique = True
preproc.connect(inputnode, 'brain_mask', brain_mask_deoblique,
'in_file')
brain_mask_reorient = pe.Node(interface=afni.Resample(),
name='brain_mask_reorient')
brain_mask_reorient.inputs.orientation = 'RPI'
brain_mask_reorient.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(brain_mask_deoblique, 'out_file',
brain_mask_reorient, 'in_file')
anat_skullstrip_orig_vol = pe.Node(interface=afni.Calc(),
name='anat_skullstrip_orig_vol')
anat_skullstrip_orig_vol.inputs.expr = 'a*step(b)'
anat_skullstrip_orig_vol.inputs.outputtype = 'NIFTI_GZ'
preproc.connect(anat_reorient, 'out_file',
anat_skullstrip_orig_vol, 'in_file_a')
preproc.connect(brain_mask_reorient, 'out_file',
anat_skullstrip_orig_vol, 'in_file_b')
preproc.connect(brain_mask_reorient, 'out_file', outputnode,
'brain_mask')
preproc.connect(anat_skullstrip_orig_vol, 'out_file', outputnode,
'brain')
elif method == 'unet':
"""
UNet
options (following numbers are default):
input_slice: 3
conv_block: 5
kernel_root: 16
rescale_dim: 256
"""
# TODO: add options to pipeline_config
train_model = UNet2d(dim_in=3, num_conv_block=5, kernel_root=16)
unet_path = check_for_s3(c.unet_model)
checkpoint = torch.load(unet_path, map_location={'cuda:0': 'cpu'})
train_model.load_state_dict(checkpoint['state_dict'])
model = nn.Sequential(train_model, nn.Softmax2d())
# create a node called unet_mask
unet_mask = pe.Node(util.Function(input_names=['model', 'cimg_in'],
output_names=['out_path'],
function=predict_volumes),
name='unet_mask')
unet_mask.inputs.model = model
preproc.connect(anat_reorient, 'out_file', unet_mask, 'cimg_in')
"""
Revised mask with ANTs
"""
# fslmaths <whole head> -mul <mask> brain.nii.gz
unet_masked_brain = pe.Node(interface=fsl.MultiImageMaths(),
name='unet_masked_brain')
unet_masked_brain.inputs.op_string = "-mul %s"
preproc.connect(anat_reorient, 'out_file', unet_masked_brain,
'in_file')
preproc.connect(unet_mask, 'out_path', unet_masked_brain,
'operand_files')
# flirt -v -dof 6 -in brain.nii.gz -ref NMT_SS_0.5mm.nii.gz -o brain_rot2atl -omat brain_rot2atl.mat -interp sinc
# TODO change it to ANTs linear transform
native_brain_to_template_brain = pe.Node(
interface=fsl.FLIRT(), name='native_brain_to_template_brain')
native_brain_to_template_brain.inputs.reference = c.template_brain_only_for_anat
native_brain_to_template_brain.inputs.dof = 6
native_brain_to_template_brain.inputs.interp = 'sinc'
preproc.connect(unet_masked_brain, 'out_file',
native_brain_to_template_brain, 'in_file')
# flirt -in head.nii.gz -ref NMT_0.5mm.nii.gz -o head_rot2atl -applyxfm -init brain_rot2atl.mat
# TODO change it to ANTs linear transform
native_head_to_template_head = pe.Node(
interface=fsl.FLIRT(), name='native_head_to_template_head')
native_head_to_template_head.inputs.reference = c.template_skull_for_anat
native_head_to_template_head.inputs.apply_xfm = True
preproc.connect(anat_reorient, 'out_file',
native_head_to_template_head, 'in_file')
preproc.connect(native_brain_to_template_brain, 'out_matrix_file',
native_head_to_template_head, 'in_matrix_file')
# fslmaths NMT_SS_0.5mm.nii.gz -bin templateMask.nii.gz
template_brain_mask = pe.Node(interface=fsl.maths.MathsCommand(),
name='template_brain_mask')
template_brain_mask.inputs.in_file = c.template_brain_only_for_anat
template_brain_mask.inputs.args = '-bin'
# ANTS 3 -m CC[head_rot2atl.nii.gz,NMT_0.5mm.nii.gz,1,5] -t SyN[0.25] -r Gauss[3,0] -o atl2T1rot -i 60x50x20 --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000
ants_template_head_to_template = pe.Node(
interface=ants.Registration(),
name='template_head_to_template')
ants_template_head_to_template.inputs.metric = ['CC']
ants_template_head_to_template.inputs.metric_weight = [1, 5]
ants_template_head_to_template.inputs.moving_image = c.template_skull_for_anat
ants_template_head_to_template.inputs.transforms = ['SyN']
ants_template_head_to_template.inputs.transform_parameters = [
(0.25, )
]
ants_template_head_to_template.inputs.interpolation = 'NearestNeighbor'
ants_template_head_to_template.inputs.number_of_iterations = [[
60, 50, 20
]]
ants_template_head_to_template.inputs.smoothing_sigmas = [[
0.6, 0.2, 0.0
]]
ants_template_head_to_template.inputs.shrink_factors = [[4, 2, 1]]
ants_template_head_to_template.inputs.convergence_threshold = [
1.e-8
]
preproc.connect(native_head_to_template_head, 'out_file',
ants_template_head_to_template, 'fixed_image')
# antsApplyTransforms -d 3 -i templateMask.nii.gz -t atl2T1rotWarp.nii.gz atl2T1rotAffine.txt -r brain_rot2atl.nii.gz -o brain_rot2atl_mask.nii.gz
template_head_transform_to_template = pe.Node(
interface=ants.ApplyTransforms(),
name='template_head_transform_to_template')
template_head_transform_to_template.inputs.dimension = 3
preproc.connect(template_brain_mask, 'out_file',
template_head_transform_to_template, 'input_image')
preproc.connect(native_brain_to_template_brain, 'out_file',
template_head_transform_to_template,
'reference_image')
preproc.connect(ants_template_head_to_template,
'forward_transforms',
template_head_transform_to_template, 'transforms')
# convert_xfm -omat brain_rot2native.mat -inverse brain_rot2atl.mat
invt = pe.Node(interface=fsl.ConvertXFM(), name='convert_xfm')
invt.inputs.invert_xfm = True
preproc.connect(native_brain_to_template_brain, 'out_matrix_file',
invt, 'in_file')
# flirt -in brain_rot2atl_mask.nii.gz -ref brain.nii.gz -o brain_mask.nii.gz -applyxfm -init brain_rot2native.mat
template_brain_to_native_brain = pe.Node(
interface=fsl.FLIRT(), name='template_brain_to_native_brain')
template_brain_to_native_brain.inputs.apply_xfm = True
preproc.connect(template_head_transform_to_template,
'output_image', template_brain_to_native_brain,
'in_file')
preproc.connect(unet_masked_brain, 'out_file',
template_brain_to_native_brain, 'reference')
preproc.connect(invt, 'out_file', template_brain_to_native_brain,
'in_matrix_file')
# fslmaths brain_mask.nii.gz -thr .5 -bin brain_mask_thr.nii.gz
refined_mask = pe.Node(interface=fsl.Threshold(),
name='refined_mask')
refined_mask.inputs.thresh = 0.5
preproc.connect(template_brain_to_native_brain, 'out_file',
refined_mask, 'in_file')
# get a new brain with mask
refined_brain = pe.Node(interface=fsl.MultiImageMaths(),
name='refined_brain')
refined_brain.inputs.op_string = "-mul %s"
preproc.connect(anat_reorient, 'out_file', refined_brain,
'in_file')
preproc.connect(refined_mask, 'out_file', refined_brain,
'operand_files')
preproc.connect(refined_mask, 'out_file', outputnode, 'brain_mask')
preproc.connect(refined_brain, 'out_file', outputnode, 'brain')
return preproc
def create_qc_snr(wf_name='qc_snr'):
wf = pe.Workflow(name=wf_name)
input_node = pe.Node(util.IdentityInterface(fields=[
'functional_preprocessed', 'functional_brain_mask',
'functional_to_anat_linear_xfm', 'anatomical_brain',
'mean_functional_in_anat'
]),
name='inputspec')
output_node = pe.Node(util.IdentityInterface(fields=[
'snr_axial_image', 'snr_sagittal_image', 'snr_histogram_image',
'snr_mean'
]),
name='outputspec')
std_dev = pe.Node(afni.TStat(args='-stdev'), name='std_dev')
std_dev.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'functional_preprocessed', std_dev, 'in_file')
wf.connect(input_node, 'functional_brain_mask', std_dev, 'mask')
std_dev_anat = pe.Node(fsl.ApplyWarp(interp='trilinear'),
name='std_dev_anat')
wf.connect(input_node, 'functional_to_anat_linear_xfm', std_dev_anat,
'premat')
wf.connect(std_dev, 'out_file', std_dev_anat, 'in_file')
wf.connect(input_node, 'anatomical_brain', std_dev_anat, 'ref_file')
snr = pe.Node(afni.Calc(expr='b/a'), name='snr')
snr.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'mean_functional_in_anat', snr, 'in_file_b')
wf.connect(std_dev_anat, 'out_file', snr, 'in_file_a')
snr_val = pe.Node(Function(input_names=['measure_file'],
output_names=['snr_storefl'],
function=cal_snr_val,
as_module=True),
name='snr_val')
wf.connect(snr, 'out_file', snr_val, 'measure_file')
hist_snr = pe.Node(Function(input_names=['measure_file', 'measure'],
output_names=['hist_path'],
function=gen_histogram,
as_module=True),
name='hist_snr')
hist_snr.inputs.measure = 'snr'
wf.connect(snr, 'out_file', hist_snr, 'measure_file')
snr_drop_percent = pe.Node(Function(
input_names=['measure_file', 'percent'],
output_names=['modified_measure_file'],
function=drop_percent,
as_module=True),
name='dp_snr')
snr_drop_percent.inputs.percent = 99
wf.connect(snr, 'out_file', snr_drop_percent, 'measure_file')
montage_snr = create_montage('montage_snr', 'red_to_blue', 'snr')
wf.connect(snr_drop_percent, 'modified_measure_file', montage_snr,
'inputspec.overlay')
wf.connect(input_node, 'anatomical_brain', montage_snr,
'inputspec.underlay')
wf.connect(montage_snr, 'outputspec.axial_png', output_node,
'snr_axial_image')
wf.connect(montage_snr, 'outputspec.sagittal_png', output_node,
'snr_sagittal_image')
wf.connect(hist_snr, 'hist_path', output_node, 'snr_histogram_image')
wf.connect(snr_val, 'snr_storefl', output_node, 'snr_mean')
return wf
name="datasource") #grabs data
datasource.inputs.base_directory = '/afs/cbs.mpg.de/projects/mar004_lsd-lemon-preproc/probands/'
datasource.inputs.template = '%s/preprocessed/lsd_resting/%s/rest_preprocessed2mni.nii.gz'
datasource.inputs.template_args['EPI_bandpassed'] = [['subject_id', 'sess_id']]
datasource.inputs.sort_filelist = True
wf.connect(subjects_infosource, "subject_id", datasource, "subject_id")
wf.connect(sess_infosource, "sess_id", datasource, "sess_id")
automask = pe.Node(interface=afni.Automask(), name='automask')
automask.inputs.dilate = 1
automask.inputs.outputtype = "NIFTI_GZ"
wf.connect(datasource, 'EPI_bandpassed', automask, 'in_file')
wf.connect(automask, 'out_file', ds, '@automask')
#extract rois with spheres
sphere = pe.Node(afni.Calc(), name="sphere")
sphere.inputs.in_file_a = fsl.Info.standard_image(
'/usr/share/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz')
sphere.inputs.outputtype = 'NIFTI_GZ'
def roi2exp(coord):
radius = 4
return "step((%d*%d)-(x+%d)*(x+%d)-(y+%d)*(y+%d)-(z+%d)*(z+%d))" % (
radius, radius, coord[0], coord[0], coord[1], coord[1], -coord[2],
-coord[2])
def roi2name(coord):
return 'roi_sphere_%s_%s_%s.nii.gz' % (str(coord[0]), str(
coord[1]), str(coord[2]))
def __init__(self, settings):
# call base constructor
super().__init__(settings)
# define input/output node
self.set_input(['T1', 'orig', 'brainmask'])
self.set_output(['T1_skullstrip', 'allineate_freesurfer2anat'])
# define datasink substitutions
self.set_subs([('_maskop40', ''), ('_calc_calc_calc_calc_calc', '')])
# 3dAllineate (FSorig)
self.allineate_orig = MapNode(afni.Allineate(
out_matrix='FSorig2MPR.aff12.1D',
overwrite=True,
outputtype='NIFTI_GZ'),
iterfield=['in_file', 'reference'],
name='3dallineate_orig')
# 3dAllineate (FSbrainmask)
self.allineate_bm = MapNode(
afni.Allineate(overwrite=True, no_pad=True, outputtype='NIFTI_GZ'),
iterfield=['in_file', 'reference', 'in_matrix'],
name='3dallineate_brainmask')
# skullstrip mprage (afni)
self.afni_skullstrip = MapNode(afni.SkullStrip(args="-orig_vol",
outputtype="NIFTI_GZ"),
iterfield=['in_file'],
name='afni_skullstrip')
# 3dcalc operations for achieving final mask
self.maskop1 = MapNode(afni.Calc(expr='step(a)',
overwrite=True,
outputtype='NIFTI_GZ'),
iterfield=['in_file_a'],
name='maskop1')
self.maskop2 = []
for n in range(3):
self.maskop2.append(
MapNode(afni.Calc(
args='-b a+i -c a-i -d a+j -e a-j -f a+k -g a-k',
expr='ispositive(a+b+c+d+e+f+g)',
overwrite=True,
outputtype='NIFTI_GZ'),
iterfield=['in_file_a'],
name='maskop2_{}'.format(n)))
# Inline function for setting up to copy IJK_TO_DICOM_REAL file attribute
self.refit_setup = MapNode(Function(input_names=['noskull_T1'],
output_names=['refit_input'],
function=lambda noskull_T1:
(noskull_T1, 'IJK_TO_DICOM_REAL')),
iterfield=['noskull_T1'],
name='refitsetup')
# 3dRefit
self.refit = MapNode(afni.Refit(),
iterfield=['in_file', 'atrcopy'],
name='3drefit')
# 3dcalc for uniform intensity
self.uniform = MapNode(afni.Calc(expr='a*and(b,b)',
overwrite=True,
outputtype='NIFTI_GZ'),
iterfield=['in_file_a', 'in_file_b'],
name='uniformintensity')
# skullstrip mprage (fsl)
self.fsl_skullstrip = MapNode(fsl.BET(),
iterfield=['in_file'],
name='fsl_skullstrip')
self.maskop3 = MapNode(
afni.Calc(expr='or(a,b,c)', overwrite=True, outputtype='NIFTI_GZ'),
iterfield=['in_file_a', 'in_file_b', 'in_file_c'],
name='maskop3')
self.maskop4 = MapNode(
afni.Calc(expr='c*and(a,b)', overwrite=True,
outputtype='NIFTI_GZ'),
iterfield=['in_file_a', 'in_file_b', 'in_file_c'],
name='maskop4')
# Convert from list to string input
self.select0T1 = Node(Function(input_names=['T1_list'],
output_names=['T1_0'],
function=lambda T1_list: T1_list[0]),
name='select0T1')
# apply bias field correction
self.biasfieldcorrect = Node(ants.N4BiasFieldCorrection(
num_threads=settings['num_threads'], copy_header=True),
name='biasfieldcorrect')
def generate_summarize_tissue_mask_ventricles_masking(
nuisance_wf,
pipeline_resource_pool,
regressor_descriptor,
regressor_selector,
mask_key,
use_ants=True,
ventricle_mask_exist=True):
# Mask CSF with Ventricles
if '{}_Unmasked'.format(mask_key) not in pipeline_resource_pool:
# reduce CSF mask to the lateral ventricles
mask_csf_with_lat_ven = pe.Node(
interface=afni.Calc(outputtype='NIFTI_GZ'),
name='{}_Ventricles'.format(mask_key))
mask_csf_with_lat_ven.inputs.expr = 'a*b'
mask_csf_with_lat_ven.inputs.out_file = 'csf_lat_ven_mask.nii.gz'
if ventricle_mask_exist:
ventricles_key = 'VentriclesToAnat'
if 'resolution' in regressor_descriptor:
ventricles_key += '_{}'.format(
regressor_descriptor['resolution'])
if ventricles_key not in pipeline_resource_pool:
transforms = pipeline_resource_pool['Transformations']
if use_ants is True:
# perform the transform using ANTS
collect_linear_transforms = pe.Node(
util.Merge(3),
name='{}_ants_transforms'.format(ventricles_key))
nuisance_wf.connect(
*(transforms['anat_to_mni_initial_xfm'] +
(collect_linear_transforms, 'in1')))
nuisance_wf.connect(*(transforms['anat_to_mni_rigid_xfm'] +
(collect_linear_transforms, 'in2')))
nuisance_wf.connect(
*(transforms['anat_to_mni_affine_xfm'] +
(collect_linear_transforms, 'in3')))
# check transform list to exclude Nonetype (missing) init/rig/affine
check_transform = pe.Node(
util.Function(input_names=['transform_list'],
output_names=[
'checked_transform_list',
'list_length'
],
function=check_transforms),
name='{0}_check_transforms'.format(ventricles_key))
nuisance_wf.connect(collect_linear_transforms, 'out',
check_transform, 'transform_list')
# generate inverse transform flags, which depends on the number of transforms
inverse_transform_flags = pe.Node(
util.Function(
input_names=['transform_list'],
output_names=['inverse_transform_flags'],
function=generate_inverse_transform_flags),
name='{0}_inverse_transform_flags'.format(
ventricles_key))
nuisance_wf.connect(check_transform,
'checked_transform_list',
inverse_transform_flags,
'transform_list')
lat_ven_mni_to_anat = pe.Node(
interface=ants.ApplyTransforms(),
name='{}_ants'.format(ventricles_key))
lat_ven_mni_to_anat.inputs.interpolation = 'NearestNeighbor'
lat_ven_mni_to_anat.inputs.dimension = 3
nuisance_wf.connect(inverse_transform_flags,
'inverse_transform_flags',
lat_ven_mni_to_anat,
'invert_transform_flags')
nuisance_wf.connect(check_transform,
'checked_transform_list',
lat_ven_mni_to_anat, 'transforms')
nuisance_wf.connect(
*(pipeline_resource_pool['Ventricles'] +
(lat_ven_mni_to_anat, 'input_image')))
nuisance_wf.connect(
*(pipeline_resource_pool[mask_key] +
(lat_ven_mni_to_anat, 'reference_image')))
pipeline_resource_pool[ventricles_key] = (
lat_ven_mni_to_anat, 'output_image')
else:
# perform the transform using FLIRT
lat_ven_mni_to_anat = pe.Node(
interface=fsl.FLIRT(),
name='{}_flirt'.format(ventricles_key))
lat_ven_mni_to_anat.inputs.interp = 'nearestneighbour'
nuisance_wf.connect(
*(transforms['mni_to_anat_linear_xfm'] +
(lat_ven_mni_to_anat, 'in_matrix_file')))
nuisance_wf.connect(
*(pipeline_resource_pool['Ventricles'] +
(lat_ven_mni_to_anat, 'in_file')))
nuisance_wf.connect(*(pipeline_resource_pool[mask_key] +
(lat_ven_mni_to_anat, 'reference')))
pipeline_resource_pool[ventricles_key] = (
lat_ven_mni_to_anat, 'out_file')
nuisance_wf.connect(*(pipeline_resource_pool[ventricles_key] +
(mask_csf_with_lat_ven, 'in_file_a')))
nuisance_wf.connect(*(pipeline_resource_pool[mask_key] +
(mask_csf_with_lat_ven, 'in_file_b')))
pipeline_resource_pool['{}_Unmasked'.format(
mask_key)] = pipeline_resource_pool[mask_key]
pipeline_resource_pool[mask_key] = (mask_csf_with_lat_ven,
'out_file')
else:
pipeline_resource_pool['{}_Unmasked'.format(
mask_key)] = pipeline_resource_pool[mask_key]
return pipeline_resource_pool
def init_falff_wf(workdir: str | Path,
feature=None,
fwhm=None,
memcalc=MemoryCalculator.default()):
"""
Calculate Amplitude of low frequency oscillations(ALFF) and
fractional ALFF maps
Returns
-------
workflow : workflow object
ALFF workflow
Notes
-----
Adapted from
<https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/alff/alff.py>
"""
if feature is not None:
name = f"{format_workflow(feature.name)}"
else:
name = "falff"
if fwhm is not None:
name = f"{name}_{int(float(fwhm) * 1e3):d}"
name = f"{name}_wf"
workflow = pe.Workflow(name=name)
# input
inputnode = pe.Node(
niu.IdentityInterface(
fields=["tags", "vals", "metadata", "bold", "mask", "fwhm"]),
name="inputnode",
)
unfiltered_inputnode = pe.Node(
niu.IdentityInterface(fields=["bold", "mask"]),
name="unfiltered_inputnode",
)
outputnode = pe.Node(niu.IdentityInterface(fields=["resultdicts"]),
name="outputnode")
if fwhm is not None:
inputnode.inputs.fwhm = float(fwhm)
elif feature is not None and hasattr(feature, "smoothing"):
inputnode.inputs.fwhm = feature.smoothing.get("fwhm")
#
make_resultdicts = pe.Node(
MakeResultdicts(tagkeys=["feature"],
imagekeys=["alff", "falff", "mask"]),
name="make_resultdicts",
)
if feature is not None:
make_resultdicts.inputs.feature = feature.name
workflow.connect(inputnode, "tags", make_resultdicts, "tags")
workflow.connect(inputnode, "vals", make_resultdicts, "vals")
workflow.connect(inputnode, "metadata", make_resultdicts, "metadata")
workflow.connect(inputnode, "mask", make_resultdicts, "mask")
workflow.connect(make_resultdicts, "resultdicts", outputnode,
"resultdicts")
#
resultdict_datasink = pe.Node(ResultdictDatasink(base_directory=workdir),
name="resultdict_datasink")
workflow.connect(make_resultdicts, "resultdicts", resultdict_datasink,
"indicts")
# standard deviation of the filtered image
stddev_filtered = pe.Node(afni.TStat(),
name="stddev_filtered",
mem_gb=memcalc.series_std_gb)
stddev_filtered.inputs.outputtype = "NIFTI_GZ"
stddev_filtered.inputs.options = "-stdev"
workflow.connect(inputnode, "bold", stddev_filtered, "in_file")
workflow.connect(inputnode, "mask", stddev_filtered, "mask")
# standard deviation of the unfiltered image
stddev_unfiltered = pe.Node(afni.TStat(),
name="stddev_unfiltered",
mem_gb=memcalc.series_std_gb)
stddev_unfiltered.inputs.outputtype = "NIFTI_GZ"
stddev_unfiltered.inputs.options = "-stdev"
workflow.connect(unfiltered_inputnode, "bold", stddev_unfiltered,
"in_file")
workflow.connect(unfiltered_inputnode, "mask", stddev_unfiltered, "mask")
falff = pe.Node(afni.Calc(), name="falff", mem_gb=memcalc.volume_std_gb)
falff.inputs.args = "-float"
falff.inputs.expr = "(1.0*bool(a))*((1.0*b)/(1.0*c))"
falff.inputs.outputtype = "NIFTI_GZ"
workflow.connect(inputnode, "mask", falff, "in_file_a")
workflow.connect(stddev_filtered, "out_file", falff, "in_file_b")
workflow.connect(stddev_unfiltered, "out_file", falff, "in_file_c")
#
merge = pe.Node(niu.Merge(2), name="merge")
workflow.connect(stddev_filtered, "out_file", merge, "in1")
workflow.connect(falff, "out_file", merge, "in2")
smooth = pe.MapNode(LazyBlurToFWHM(outputtype="NIFTI_GZ"),
iterfield="in_file",
name="smooth")
workflow.connect(merge, "out", smooth, "in_file")
workflow.connect(inputnode, "mask", smooth, "mask")
workflow.connect(inputnode, "fwhm", smooth, "fwhm")
zscore = pe.MapNode(ZScore(),
iterfield="in_file",
name="zscore",
mem_gb=memcalc.volume_std_gb)
workflow.connect(smooth, "out_file", zscore, "in_file")
workflow.connect(inputnode, "mask", zscore, "mask")
split = pe.Node(niu.Split(splits=[1, 1]), name="split")
workflow.connect(zscore, "out_file", split, "inlist")
workflow.connect(split, "out1", make_resultdicts, "alff")
workflow.connect(split, "out2", make_resultdicts, "falff")
return workflow
def create_pipeline_graph(pipeline_name, graph_file,
graph_kind='hierarchical'):
"""Creates pipeline graph for a given piepline.
Parameters
----------
pipeline_name : one of {'anat_to_common_rigid', 'anat_to_common_affine',
'anat_to_common_nonlinear'}
Pipeline name.
graph_file : str.
Path to save the graph image to.
graph_kind : one of {'orig', 'hierarchical', 'flat', 'exec', 'colored'}, optional.
The kind of the graph, passed to
nipype.pipeline.workflows.Workflow().write_graph
"""
pipeline_names = ['anats_to_common_rigid', 'anats_to_common_affine',
'anats_to_common_nonlinear']
if pipeline_name not in pipeline_names:
raise NotImplementedError(
'Pipeline name must be one of {0}, you entered {1}'.format(
pipeline_names, pipeline_name))
graph_kinds = ['orig', 'hierarchical', 'flat', 'exec', 'colored']
if graph_kind not in graph_kinds:
raise ValueError(
'Graph kind must be one of {0}, you entered {1}'.format(
graph_kinds, graph_kind))
workflow = pe.Workflow(name=pipeline_name)
#######################################################################
# Specify rigid body registration pipeline steps
unifize = pe.Node(interface=afni.Unifize(), name='bias_correct')
clip_level = pe.Node(interface=afni.ClipLevel(),
name='compute_mask_threshold')
compute_mask = pe.Node(interface=interfaces.MathMorphoMask(),
name='compute_brain_mask')
apply_mask = pe.Node(interface=afni.Calc(), name='apply_brain_mask')
center_mass = pe.Node(interface=afni.CenterMass(),
name='compute_and_set_cm_in_header')
refit_copy = pe.Node(afni.Refit(), name='copy_cm_in_header')
tcat1 = pe.Node(afni.TCat(), name='concatenate_across_individuals1')
tstat1 = pe.Node(afni.TStat(), name='compute_average1')
undump = pe.Node(afni.Undump(), name='create_empty_template')
refit_set = pe.Node(afni.Refit(), name='set_cm_in_header')
resample1 = pe.Node(afni.Resample(), name='resample1')
resample2 = pe.Node(afni.Resample(), name='resample2')
shift_rotate = pe.Node(afni.Allineate(), name='shift_rotate')
apply_allineate1 = pe.Node(afni.Allineate(), name='apply_transform1')
tcat2 = pe.Node(afni.TCat(), name='concatenate_across_individuals2')
tstat2 = pe.Node(afni.TStat(), name='compute_average2')
tcat3 = pe.Node(afni.TCat(), name='concatenate_across_individuals3')
tstat3 = pe.Node(afni.TStat(), name='compute_average3')
workflow.add_nodes([unifize, clip_level, compute_mask, apply_mask,
center_mass,
refit_copy, tcat1, tstat1, undump, refit_set,
resample1, resample2, shift_rotate, apply_allineate1,
tcat2, tstat2, tcat3, tstat3])
#######################################################################
# and connections
workflow.connect(unifize, 'out_file', clip_level, 'in_file')
workflow.connect(clip_level, 'clip_val',
compute_mask, 'intensity_threshold')
workflow.connect(unifize, 'out_file', compute_mask, 'in_file')
workflow.connect(compute_mask, 'out_file', apply_mask, 'in_file_a')
workflow.connect(unifize, 'out_file', apply_mask, 'in_file_b')
workflow.connect(apply_mask, 'out_file',
center_mass, 'in_file')
workflow.connect(unifize, 'out_file', refit_copy, 'in_file')
workflow.connect(center_mass, 'out_file',
refit_copy, 'duporigin_file')
workflow.connect(center_mass, 'out_file', tcat1, 'in_files')
workflow.connect(tcat1, 'out_file', tstat1, 'in_file')
workflow.connect(tstat1, 'out_file', undump, 'in_file')
workflow.connect(undump, 'out_file', refit_set, 'in_file')
workflow.connect(refit_set, 'out_file', resample1, 'master')
workflow.connect(refit_copy, 'out_file', resample1, 'in_file')
workflow.connect(refit_set, 'out_file', resample2, 'master')
workflow.connect(center_mass, 'out_file', resample2, 'in_file')
workflow.connect(resample2, 'out_file', tcat2, 'in_files')
workflow.connect(tcat2, 'out_file', tstat2, 'in_file')
workflow.connect(tstat2, 'out_file', shift_rotate, 'reference')
workflow.connect(resample2, 'out_file', shift_rotate, 'in_file')
workflow.connect(tstat2, 'out_file', apply_allineate1, 'master')
workflow.connect(resample1, 'out_file',
apply_allineate1, 'in_file')
workflow.connect(shift_rotate, 'out_matrix',
apply_allineate1, 'in_matrix')
workflow.connect(apply_allineate1, 'out_file', tcat3, 'in_files')
workflow.connect(tcat3, 'out_file', tstat3, 'in_file')
if pipeline_name in ['anats_to_common_affine',
'anat_to_common_nonlinear']:
mask = pe.Node(afni.MaskTool(), name='generate_count_mask')
allineate = pe.Node(afni.Allineate(), name='allineate')
catmatvec = pe.Node(afni.CatMatvec(), name='concatenate_transforms')
apply_allineate2 = pe.Node(afni.Allineate(), name='apply_transform2')
tcat3 = pe.Node(
afni.TCat(), name='concatenate_across_individuals4')
tstat3 = pe.Node(afni.TStat(), name='compute_average4')
workflow.add_nodes([mask, allineate, catmatvec, apply_allineate2,
tcat3, tstat3])
workflow.connect(tcat2, 'out_file', mask, 'in_file')
workflow.connect(mask, 'out_file', allineate, 'weight')
workflow.connect(apply_allineate1, 'out_file',
allineate, 'in_file')
workflow.connect(allineate, 'out_matrix',
catmatvec, 'in_file')
#XXX how can we enter multiple files ?
workflow.connect(catmatvec, 'out_file',
apply_allineate2, 'in_matrix')
workflow.connect(resample1, 'out_file',
apply_allineate2, 'in_file')
workflow.connect(apply_allineate2, 'out_file', tcat3, 'in_files')
workflow.connect(tcat3, 'out_file', tstat3, 'in_file')
if pipeline_name == 'anats_to_common_nonlinear':
pass
graph_file_root, graph_file_ext = os.path.splitext(graph_file)
if graph_file_ext:
_ = workflow.write_graph(graph2use=graph_kind,
format=graph_file_ext[1:],
dotfilename=graph_file_root)
else:
_ = workflow.write_graph(graph2use=graph_kind,
dotfilename=graph_file_root)