smriprep.interfaces.templateflow module
Interfaces to get templates from TemplateFlow.
- class smriprep.interfaces.templateflow.TemplateDesc(from_file=None, resource_monitor=None, **inputs)[source]
Bases:
SimpleInterface
Select template description and name pairs.
This interface is necessary to ensure the good functioning with iterables and JoinNodes.
>>> select = TemplateDesc(template='MNI152NLin2009cAsym') >>> result = select.run() >>> result.outputs.name 'MNI152NLin2009cAsym'
>>> result.outputs.spec {}
>>> select = TemplateDesc(template='MNIPediatricAsym:cohort-2') >>> result = select.run() >>> result.outputs.name 'MNIPediatricAsym'
>>> result.outputs.spec {'cohort': '2'}
- Mandatory Inputs:
template (a string) – Univocal template identifier.
- Outputs:
name (a string) – Template identifier.
spec (a dictionary with keys which are any value and with values which are any value) – Template arguments.
- class smriprep.interfaces.templateflow.TemplateFlowSelect(from_file=None, resource_monitor=None, **inputs)[source]
Bases:
SimpleInterface
Select TemplateFlow elements.
>>> select = TemplateFlowSelect(resolution=1) >>> select.inputs.template = 'MNI152NLin2009cAsym' >>> result = select.run() >>> result.outputs.t1w_file '.../tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz'
>>> result.outputs.brain_mask '.../tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz'
>>> select = TemplateFlowSelect() >>> select.inputs.template = 'MNIPediatricAsym' >>> select.inputs.template_spec = {'cohort': 5, 'resolution': 1} >>> result = select.run() >>> result.outputs.t1w_file '.../tpl-MNIPediatricAsym_cohort-5_res-1_T1w.nii.gz'
>>> select = TemplateFlowSelect(resolution=2) >>> select.inputs.template = 'MNIPediatricAsym:cohort-5' >>> select.inputs.template_spec = {'resolution': 1} >>> result = select.run() >>> result.outputs.t1w_file '.../tpl-MNIPediatricAsym_cohort-5_res-2_T1w.nii.gz'
>>> select = TemplateFlowSelect() >>> select.inputs.template = 'MNIPediatricAsym:cohort-2' >>> select.inputs.template_spec = {'cohort': 5, 'resolution': 1} >>> result = select.run() >>> result.outputs.t1w_file '.../tpl-MNIPediatricAsym_cohort-5_res-1_T1w.nii.gz'
>>> select = TemplateFlowSelect() >>> select.inputs.template = 'MNI305' >>> select.inputs.template_spec = {'resolution': 1} >>> result = select.run() >>> result.outputs.t1w_file '.../tpl-MNI305_T1w.nii.gz'
- Mandatory Inputs:
template (a string) – Template ID.
- Optional Inputs:
atlas (a list of items which are a string) – Specify an atlas.
cohort (a list of items which are a string or an integer) – Specify a cohort.
resolution (a list of items which are an integer) – Specify a template resolution index.
template_spec (a dictionary with keys which are a value of class ‘str’ and with values which are any value) – Template specifications. (Nipype default value:
{'atlas': None, 'cohort': None}
)
- Outputs:
brain_mask (a pathlike object or string representing an existing file) – Template’s brain mask.
t1w_file (a pathlike object or string representing an existing file) – T1w template.