mia_processes.pipelines.preprocess package

The various pipelines used for the pre-treatment stage.

Submodules

mia_processes.pipelines.preprocess.anat_airmask module

The Anat_airmask pipeline.

class mia_processes.pipelines.preprocess.anat_airmask.Anat_airmask(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Compute rotation mask, air mask, artifact mask and hat mask for structural data

Following step 1 from [Mortamet2009]

Please, see the complete documentation for the Anat_airmask pipeline in the mia_processes website

Note

  • Type ‘Anat_airmask.help()’ for a full description of this process parameters.

  • Type ‘<Anat_airmask>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Anat_airmask>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.anat_headmask module

The Anat_headmask pipeline..

class mia_processes.pipelines.preprocess.anat_headmask.Anat_headmask(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Compute head mask from skull stripped structural image using “Denoise” from Dipy

Please, see the complete documentation for the Anat_headmask pipeline in the mia_processes website

Note

  • Type ‘Anat_headmask.help()’ for a full description of this process parameters.

  • Type ‘<Anat_headmask>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Anat_headmask>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.anat_mni_tpms module

The Anat_mni_tpms pipeline.

class mia_processes.pipelines.preprocess.anat_mni_tpms.Anat_mni_tpms(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Get templates tissues probability map (white matter - WM -, grey matter - GM - and cerebrospinal - CSF -)

From ‘MNI152NLin2009cAsym’ template (resolution 1 mm) and register them in subject space.

Adapted from mriqc anatomical workflow.

Please, see the complete documentation for the Anat_mni_tpms pipeline in the mia_processes website

Note

  • Type ‘Anat_mni_tpms.help()’ for a full description of this process parameters.

  • Type ‘<Anat_mni_tpms>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Anat_mni_tpms>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.anat_skullstrip module

The Anat_skullstrip pipeline.

class mia_processes.pipelines.preprocess.anat_skullstrip.Anat_skullstrip(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Bias correction and skull stripping of a structural image

Please, see the complete documentation for the Anat_skullstrip pipeline in the mia_processes website

Note

  • Type ‘Anat_skullstrip.help()’ for a full description of this process parameters.

  • Type ‘<Anat_skullstrip>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Anat_skullstrip>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.anat_skullstrip_synthstrip module

The .Anat_skullstrip_synthstrip pipeline.

class mia_processes.pipelines.preprocess.anat_skullstrip_synthstrip.Anat_skullstrip_synthstrip(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Create a brain-extraction workflow using SynthStrip (Freesurfer)

Adapted from mriqc v22.06 synthstrip workflow

Please, see the complete documentation for the Anat_skullstrip_synthstrip pipeline in the mia_processes website

Note

  • Type ‘Anat_skullstrip_synthstrip.help()’ for a full description of this process parameters.

  • Type ‘<Anat_skullstrip_synthstrip>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Anat_skullstrip_synthstrip>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.anat_spatial_norm module

The Anat_spatial_norm pipeline.

class mia_processes.pipelines.preprocess.anat_spatial_norm.Anat_spatial_norm(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Spatial normalization to MNI (using ‘MNI152NLin2009cAsym’ template)

Adapted from mriqc 22.06 anatomical workflow

Please, see the complete documentation for the Anat_spatial_norm pipeline in the mia_processes website

Note

  • Type ‘Anat_spatial_norm.help()’ for a full description of this process parameters.

  • Type ‘<Anat_spatial_norm>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Anat_spatial_norm>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.bold_hmc module

The Bold_hmc pipeline.

class mia_processes.pipelines.preprocess.bold_hmc.Bold_hmc(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Head-motion correction based on 3dvolreg from AFNI

Please, see the complete documentation for the Bold_hmc pipeline in the mia_processes website

Note

  • Type ‘Bold_hmc.help()’ for a full description of this process parameters.

  • Type ‘<Bold_hmc>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Bold_hmc>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.bold_mni_align module

The Bold_mni_align pipeline.

class mia_processes.pipelines.preprocess.bold_mni_align.Bold_mni_align(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Registered a mean functional image EPI in MNI space

For checking out registration.

Please, see the complete documentation for the Bold_mni_align pipeline in the mia_processes website

Note

  • Type ‘Bold_mni_align.help()’ for a full description of this process parameters.

  • Type ‘<Bold_mni_align>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Bold_mni_align>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.bold_spatial_preprocessing1 module

The pipelines library of the mia_processes package.

The objective of this module is to propose pipelines built from atomic bricks or other pipelines provided in the mia_processes library.

Contains:
Class:

  • Bold_spatial_preprocessing1

class mia_processes.pipelines.preprocess.bold_spatial_preprocessing1.Bold_spatial_preprocessing1(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Data pre-processing for cerebrovascular reserve analysis (CVR)

Please, see the complete documentation for the Bold_spatial_preprocessing1 brick in the mia_processes website

Note

  • Type ‘Bold_spatial_preprocessing1.help()’ for a full description of this process parameters.

  • Type ‘<Bold_spatial_preprocessing1>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Bold_spatial_preprocessing1>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.bold_spatial_preprocessing2 module

The pipelines library of the mia_processes package.

The objective of this module is to propose pipelines built from atomic bricks or other pipelines provided in the mia_processes library.

Contains:
Class:

  • Bold_spatial_preprocessing2

class mia_processes.pipelines.preprocess.bold_spatial_preprocessing2.Bold_spatial_preprocessing2(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Bold data pre-processing

Please, see the complete documentation for the Bold_spatial_preprocessing2 brick in the mia_processes website

Note

  • Type ‘Bold_spatial_preprocessing2.help()’ for a full description of this process parameters.

  • Type ‘<Bold_spatial_preprocessing2>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Bold_spatial_preprocessing2>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.dwi_fod_msmt_csd module

The pipelines library of the mia_processes package.

The objective of this module is to propose pipelines built from atomic bricks or other pipelines provided in the mia_processes library.

Contains:
Class:

  • Dwi_fod_msmt_csd

class mia_processes.pipelines.preprocess.dwi_fod_msmt_csd.Dwi_fod_msmt_csd(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

DWI fiber orientation distribution

Please, see the complete documentation for the Dwi_fod_msmt_csd pipeline in the mia_processes website

Note

  • Type ‘Dwi_fod_msmt_csd.help()’ for a full description of this process parameters.

  • Type ‘<Dwi_fod_msmt_csd>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Dwi_fod_msmt_csd>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.dwipreprocessing module

The pipelines library of the mia_processes package.

The objective of this module is to propose pipelines built from atomic bricks or other pipelines provided in the mia_processes library.

Contains:
Class:

  • Dwi_preprocessing

class mia_processes.pipelines.preprocess.dwi_preprocessing.Dwi_preprocessing(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

DWI preprocessing with reverse b0

Please, see the complete documentation for the Dwi_preprocessing pipeline in the mia_processes website

Note

  • Type ‘Dwi_preprocessing.help()’ for a full description of this process parameters.

  • Type ‘<Dwi_preprocessing>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Dwi_preprocessing>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline

mia_processes.pipelines.preprocess.spatial_mask module

The module for the Spatial_mask pipeline.

Contains:
Class:

  • Spatial_mask

class mia_processes.pipelines.preprocess.spatial_mask.Spatial_mask(autoexport_nodes_parameters=None, **kwargs)[source]

Bases: Pipeline

Makes the grey matter native mask for cerebrovascular reserve analyse

Please, see the complete documentation for the Spatial_mask brick in the mia_processes website

Note

  • Type ‘Spatial_mask.help()’ for a full description of this process parameters.

  • Type ‘<Spatial_mask>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Spatial_mask>.get_output_spec()’ for a full description of this process output trait types.

pipeline_definition()[source]

Building the pipeline