cmp.project module

Definition of classes and functions for handling non-GUI general events.

class cmp.project.CMP_Project_Info[source]

Bases: traits.has_traits.HasTraits

Class used to store all properties of a processing project.

base_directory

BIDS dataset root directory

Type

traits.Directory

output_directory

Output directory

Type

traits.Directory

bids_layout

Instance of pybids BIDSLayout

Type

bids.BIDSLayout

subjects

List of subjects in the dataset

Type

traits.List

subject

Subject being processed in the form sub-XX

subject_sessions

List of sessions for the subject being processed

Type

traits.List

subject_session

Session of the subject being processed in the form ses-YY

Type

trait.Str

diffusion_imaging_model

Diffusion imaging model that can be ‘DSI’, ‘DTI’, ‘HARDI’ or ‘multishell’

Type

traits.Str

dmri_bids_acqs

List diffusion imaging models extracted from acq-<label> filename part.

Type

traits.List

dmri_bids_acq

Diffusion imaging model being processed

anat_runs

List of run labels for T1w scans with multiple runs

Type

traits.List

anat_run

Run being processed for T1w scans with multiple runs

Type

traits.Str

dmri_runs

List of run labels for DWI scans with multiple runs

Type

traits.List

dmri_run

Run being processed for DWI scans with multiple runs

Type

traits.Str

fmri_runs

List of run labels for fMRI scans with multiple runs

Type

traits.List

fmri_run

Run being processed for fMRI scans with multiple runs

Type

traits.Str

parcellation_scheme

Parcellation scheme used (Default: ‘Lausanne2008’)

Type

traits.Str

atlas_info

Dictionary storing parcellation atlas information See ParcellationStage for more details

Type

traits.Dict

freesurfer_subjects_dir

Freesurfer subjects directory

Type

traits.Str

freesurfer_subject_id

Freesurfer subject ID

Type

traits.Str

t1_available

True if T1w scans were found (Default: False)

Type

Bool

dmri_available

True if DWI scans were found (Default: False)

Type

Bool

fmri_available

True if fMRI scans were found (Default: False)

Type

Bool

anat_config_error_msg

Error message for the anatomical pipeline configuration file

Type

traits.Str

anat_config_to_load

Path to a configuration file for the anatomical pipeline

Type

traits.Str

anat_available_config

List of configuration files for the anatomical pipeline

Type

traits.List

anat_stage_names

List of anatomical pipeline stage names

Type

traits.List

anat_custom_last_stage

Custom last anatomical pipeline stage to be processed

Type

traits.Str

dmri_config_error_msg

Error message for the diffusion pipeline configuration file

Type

traits.Str

dmri_config_to_load

Path to a configuration file for the diffusion pipeline

Type

traits.Str

dmri_available_config

List of configuration files for the anatomical pipeline

Type

traits.List

dmri_stage_names

List of diffusion pipeline stage names

Type

traits.List

dmri_custom_last_stage

Custom last diffusion pipeline stage to be processed

Type

traits.Str

fmri_config_error_msg

Error message for the fMRI pipeline configuration file

Type

traits.Str

fmri_config_to_load

Path to a configuration file for the fMRI pipeline

Type

traits.Str

fmri_available_config

List of configuration files for the fMRI pipeline

Type

traits.List

fmri_stage_names

List of fMRI pipeline stage names

Type

traits.List

fmri_custom_last_stage

Custom last fMRI pipeline stage to be processed

Type

traits.Str

number_of_cores

Number of cores used by Nipype workflow execution engine to distribute independent processing nodes (Must be in the range of your local resources)

Type

int

cmp.project.init_anat_project(project_info, is_new_project, debug=False)[source]

Initialize the anatomical processing pipeline.

Parameters

  • project_info (cmp.project.CMP_Project_Info) – Instance of cmp.project.CMP_Project_Info object

  • is_new_project (bool) – Specify if it corresponds or not to a new project. If True, it will create initial pipeline configuration files.

  • debug (bool) – If True, display extra prints to support debugging

Returns

anat_pipeline – AnatomicalPipeline object instance

Return type

Instance(cmp.pipelines.anatomical.anatomical.AnatomicalPipeline)

cmp.project.init_dmri_project(project_info, bids_layout, is_new_project, gui=True, debug=False)[source]

Initialize the diffusion processing pipeline.

Parameters

  • project_info (cmp.project.CMP_Project_Info) – Instance of cmp.project.CMP_Project_Info object

  • bids_layout (bids.BIDSLayout) – Instance of BIDSLayout object

  • is_new_project (bool) – Specify if it corresponds or not to a new project. If True, it will create initial pipeline configuration files.

  • gui (bool) – Might be obsolete and removed in future versions

  • debug (bool) – If True, display extra prints to support debugging

Returns

dmri_pipeline – DiffusionPipeline object instance

Return type

Instance(cmp.pipelines.diffusion.diffusion.DiffusionPipeline)

cmp.project.init_fmri_project(project_info, bids_layout, is_new_project, gui=True, debug=False)[source]

Initialize the fMRI processing pipeline.

Parameters

  • project_info (cmp.project.CMP_Project_Info) – Instance of cmp.project.CMP_Project_Info object

  • bids_layout (bids.BIDSLayout) – Instance of BIDSLayout object

  • is_new_project (bool) – Specify if it corresponds or not to a new project. If True, it will create initial pipeline configuration files.

  • gui (bool) – Might be obsolete and removed in future versions

  • debug (bool) – If True, display extra prints to support debugging

Returns

fmri_pipeline – fMRIPipeline object instance

Return type

Instance(cmp.pipelines.functional.fMRI.fMRIPipeline)

cmp.project.refresh_folder(bids_directory, derivatives_directory, subject, input_folders, session=None)[source]

Creates (if needed) the folder hierarchy.

Parameters

  • bids_directory (os.path) – BIDS dataset root directory

  • derivatives_directory (os.path) – Output (derivatives) directory

  • subject (string) – BIDS subject label (sub-XX)

  • input_folders (List of string) – List of folder to be created in derivatives_directory/’cmp’/subject

  • session (string) – BIDS session label (ses-YY)

cmp.project.run_individual(bids_dir, output_dir, participant_label, session_label, anat_pipeline_config, dwi_pipeline_config, func_pipeline_config, number_of_threads=1)[source]

Function that creates the processing pipeline for complete coverage.

Parameters

  • bids_dir (string) – BIDS dataset root directory

  • output_dir (string) – Output (derivatives) directory

  • participant_label (string) – BIDS participant / subject label (sub-XX)

  • session_label (string) – BIDS session label (ses-XX)

  • anat_pipeline_config (string) – Path to anatomical pipeline configuration file

  • dwi_pipeline_config (string) – Path to diffusion pipeline configuration file

  • func_pipeline_config (string) – Path to fMRI pipeline configuration file

  • number_of_threads (int) – Number of threads used by programs relying on the OpenMP library

cmp.project.update_anat_last_processed(project_info, pipeline)[source]

Update last processing information of a AnatomicalPipeline.

Parameters
cmp.project.update_dmri_last_processed(project_info, pipeline)[source]

Update last processing information of an DiffusionPipeline.

Parameters
cmp.project.update_fmri_last_processed(project_info, pipeline)[source]

Update last processing information of an fMRIPipeline.

Parameters