cmp.pipelines.anatomical.anatomical module
Anatomical pipeline Class definition.
- class cmp.pipelines.anatomical.anatomical.AnatomicalPipeline(project_info)[source]
Bases:
cmp.pipelines.common.Pipeline
Class that extends a
Pipeline
and represents the processing pipeline for structural MRI.It is composed of the segmentation stage that performs FreeSurfer recon-all and the parcellation stage that creates the Lausanne brain parcellations.
See also
cmp.stages.segmentation.segmentation.SegmentationStage
,cmp.stages.parcellation.parcellation.ParcellationStage
- check_config()[source]
Check if custom white matter mask and custom atlas files specified in the configuration exist.
- Returns
message – String empty if all the checks pass, otherwise it contains the error message
- Return type
string
- check_input(layout, gui=True)[source]
Check if inputs of the anatomical pipeline are available.
- Parameters
layout (bids.BIDSLayout) – Instance of BIDSLayout
gui (traits.Bool) – Boolean used to display different messages but not really meaningful anymore since the GUI components have been migrated to
cmp.bidsappmanager
- Returns
valid_inputs – True if inputs are available
- Return type
traits.Bool
- check_output()[source]
Check if outputs of an
AnatomicalPipeline
are available.- Returns
valid_output <Bool> – True if all outputs are found
error_message <string> – Error message if an output is not found.
- create_datagrabber_node(base_directory)[source]
Create the appropriate Nipype DataGrabber node.`
- Parameters
base_directory (Directory) – Main CMP output directory of a subject e.g.
/output_dir/cmp/sub-XX/(ses-YY)
- Returns
datasource – Output Nipype Node with
DataGrabber
interface- Return type
Output Nipype DataGrabber Node
- create_datasinker_node(base_directory)[source]
Create the appropriate Nipype DataSink node depending on the
parcellation_scheme
- Parameters
base_directory (Directory) – Main CMP output directory of a subject e.g.
/output_dir/cmp/sub-XX/(ses-YY)
- Returns
sinker – Output Nipype Node with
DataSink
interface- Return type
Output Nipype DataSink Node
- create_pipeline_flow(cmp_deriv_subject_directory, nipype_deriv_subject_directory)[source]
Create the pipeline workflow.
- Parameters
cmp_deriv_subject_directory (Directory) – Main CMP output directory of a subject e.g.
/output_dir/cmp/sub-XX/(ses-YY)
nipype_deriv_subject_directory (Directory) – Intermediate Nipype output directory of a subject e.g.
/output_dir/nipype/sub-XX/(ses-YY)
- Returns
anat_flow – An instance of
nipype.pipeline.engine.Workflow
- Return type
nipype.pipeline.engine.Workflow
- define_custom_mapping(custom_last_stage)[source]
Define the pipeline to be executed until a specific stages.
Not used yet by CMP3.
- Parameters
custom_last_stage (string) – Last stage to execute. Valid values are “Segmentation” and “Parcellation”
- global_conf = <cmp.pipelines.anatomical.anatomical.GlobalConfig object>
- init_subject_derivatives_dirs()[source]
Return the paths to Nipype and CMP derivatives folders of a given subject / session.
Notes
self.subject
is updated to “sub-<participant_label>_ses-<session_label>” when subject has multiple sessions.
- input_folders = ['anat']
- now = '20250204_1005'
- ordered_stage_list = ['Segmentation', 'Parcellation']
- class cmp.pipelines.anatomical.anatomical.GlobalConfig[source]
Bases:
traits.has_traits.HasTraits
Global pipeline configurations.
- process_type
Processing pipeline type
- Type
‘anatomical’
- subjects
List of subjects ID (in the form
sub-XX
)- Type
traits.List
- subject
Subject to be processed (in the form
sub-XX
)- Type
traits.Str
- subject_session
Subject session to be processed (in the form
ses-YY
)- Type
traits.Str