cmp.stages.diffusion.diffusion module
Definition of config and stage classes for diffusion reconstruction and tractography.
- class cmp.stages.diffusion.diffusion.DiffusionConfig[source]
Bases:
traits.has_traits.HasTraits
Class used to store configuration parameters of a
DiffusionStage
instance.- diffusion_imaging_model_editor
Available diffusion imaging models
- Type
[‘DSI’, ‘DTI’, ‘HARDI’, ‘multishell’]
- diffusion_imaging_model
Selected diffusion imaging model (Default: ‘DTI’)
- Type
traits.Str
- dilate_rois
Dilate parcellation regions-of-interest (Default: True)
- Type
traits.Bool
- dilation_kernel
Type of dilation kernel to used
- Type
traits.Enum([‘Box’, ‘Gauss’, ‘Sphere’])
- dilation_radius
Radius of the dilation kernel
- Type
traits.Enum([1, 2, 3, 4])
- recon_processing_tool_editor
List of processing tools available for diffusion signal reconstruction
- Type
[‘Dipy’, ‘MRtrix’]
- tracking_processing_tool_editor
List of processing tools available for tractography
- Type
[‘Dipy’, ‘MRtrix’]
- processing_tool_editor
List of processing tools available for diffusion signal reconstruction and tractography
- Type
[‘Dipy’, ‘MRtrix’]
- recon_processing_tool
Processing tool to use for diffusion signal modeling (Default: ‘MRtrix’)
- Type
traits.Str
- tracking_processing_tool
Processing tool to use for tractography (Default: ‘MRtrix’)
- Type
traits.Str
- custom_track_file
Custom tractogram file to used as input to the connectome stage (obsolete)
- Type
traits.File
- dipy_recon_config
Configuration instance of the Dipy reconstruction stage
- Type
Instance(HasTraits)
- mrtrix_recon_config
Configuration instance of the MRtrix3 reconstruction stage
- Type
Instance(HasTraits)
- dipy_tracking_config
Configuration instance of the Dipy tracking (tractography) stage
- Type
Instance(HasTraits)
- mrtrix_tracking_config
Configuration instance of the MRtrix3 tracking (tractography) stage
- Type
Instance(HasTraits)
- diffusion_model_editor
List of types of available local tractography algorithms.
- Type
[‘Deterministic’, ‘Probabilistic’]
- diffusion_model
Type of local tractography algorithm to use. (Default: ‘Probabilistic’)
- Type
traits.Str
See also
cmp.stages.diffusion.reconstruction.DipyReconConfig
,cmp.stages.diffusion.reconstruction.MRtrixReconConfig
,cmp.stages.diffusion.tracking.DipyTrackingConfig
,cmp.stages.diffusion.tracking.MRtrixTrackingConfig
,cmp.stages.diffusion.diffusion.DiffusionStage
- update_dipy_tracking_SD(new)[source]
Update
SD
ofdipy_tracking_config
whenlocal_model
is updated.- Parameters
new (string) – New value of
local_model
- class cmp.stages.diffusion.diffusion.DiffusionStage(bids_dir, output_dir)[source]
Bases:
cmp.stages.common.Stage
Class that represents the diffusion stage of a
DiffusionPipeline
.The diffusion stage workflow is composed of two sub-workflows: 1.
recon_flow
that estimates tensors or fiber orientation distribution functions from dMRI, 2.track_flow
that runs tractography from the output ofrecon_flow
.- create_workflow()[source]
Create the workflow of the
DiffusionStage
See also
cmp.pipelines.diffusion.diffusion.DiffusionPipeline
,cmp.stages.diffusion.diffusion.DiffusionConfig
,cmp.stages.diffusion.reconstruction.DipyReconConfig
,cmp.stages.diffusion.reconstruction.MRtrixReconConfig
,cmp.stages.diffusion.tracking.DipyTrackingConfig
,cmp.stages.diffusion.tracking.MRtrixTrackingConfig
,cmp.stages.diffusion.reconstruction.create_dipy_recon_flow
,cmp.stages.diffusion.reconstruction.create_mrtrix_recon_flow
,cmp.stages.diffusion.tracking.create_dipy_tracking_flow
,cmp.stages.diffusion.tracking.create_mrtrix_tracking_flow
- create_workflow(flow, inputnode, outputnode)[source]
Create the stage worflow.
- Parameters
flow (nipype.pipeline.engine.Workflow) – The nipype.pipeline.engine.Workflow instance of the Diffusion pipeline
inputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the inputs of the stage
outputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the outputs of the stage
- cmp.stages.diffusion.diffusion.strip_suffix(file_input, prefix)[source]
Extract path of
file_input
and addprefix
to generate a prefix path for outputs.- Parameters
file_input (os.path.abspath) – Absolute path to an input file
prefix (os.path) – Prefix to used in the generation of the output prefix path.
- Returns
out_prefix_path – The generated prefix path
- Return type
os.path