mia_processes.bricks.preprocess.ants package

The atomic calculations from ants.

Submodules

mia_processes.bricks.preprocess.ants.processes module

The ants preprocess library of the mia_processes package.

The purpose of this module is to customise the main ants preprocessing bricks provided by nipype and to correct some things that do not work directly in populse_mia.

Contains:
Class:

  • AffineInitializer

  • ApplyTransforms

  • N4BiasFieldCorrection

  • Registration

class mia_processes.bricks.preprocess.ants.processes.AffineInitializer[source]

Bases: ProcessMIA

A multi-start optimizer for affine registration

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

Note

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

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

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

__init__()[source]

Dedicated to the attributes initialisation/instantiation.

The input and output plugs are defined here. The special ‘self.requirement’ attribute (optional) is used to define the third-party products necessary for the running of the brick.

list_outputs(is_plugged=None, iteration=False)[source]

Dedicated to the initialisation step of the brick.

The main objective of this method is to produce the outputs of the bricks (self.outputs) and the associated tags (self.inheritance_dic), if defined here. In order not to include an output in the database, this output must be a value of the optional key ‘notInDb’ of the self.outputs dictionary. To work properly this method must return self.make_initResult() object.

Parameters:

  • is_plugged – the state, linked or not, of the plugs.

  • iteration – the state, iterative or not, of the process.

Returns:

a dictionary with requirement, outputs and inheritance_dict.

run_process_mia()[source]

Dedicated to the process launch step of the brick.

class mia_processes.bricks.preprocess.ants.processes.ApplyTransforms[source]

Bases: ProcessMIA

Transforms an image according to a reference image and transformation (or set of transformation)

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

Note

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

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

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

__init__()[source]

Dedicated to the attributes initialisation/instantiation.

The input and output plugs are defined here. The special ‘self.requirement’ attribute (optional) is used to define the third-party products necessary for the running of the brick.

list_outputs(is_plugged=None, iteration=False)[source]

Dedicated to the initialisation step of the brick.

The main objective of this method is to produce the outputs of the bricks (self.outputs) and the associated tags (self.inheritance_dic), if defined here. In order not to include an output in the database, this output must be a value of the optional key ‘notInDb’ of the self.outputs dictionary. To work properly this method must return self.make_initResult() object.

Parameters:

  • is_plugged – the state, linked or not, of the plugs.

  • iteration – the state, iterative or not, of the process.

Returns:

a dictionary with requirement, outputs and inheritance_dict.

run_process_mia()[source]

Dedicated to the process launch step of the brick.

class mia_processes.bricks.preprocess.ants.processes.N4BiasFieldCorrection[source]

Bases: ProcessMIA

N4 Bias field correction

Please, see the complete documentation for the N4BiasFieldCorrection brick in the mia_processes website

Note

  • Type ‘N4BiasFieldCorrection.help()’ for a full description of this process parameters.

  • Type ‘<N4BiasFieldCorrection>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<N4BiasFieldCorrection>.get_output_spec()’ for a full description of this process output trait types.

__init__()[source]

Dedicated to the attributes initialisation/instantiation.

The input and output plugs are defined here. The special ‘self.requirement’ attribute (optional) is used to define the third-party products necessary for the running of the brick.

list_outputs(is_plugged=None, iteration=False)[source]

Dedicated to the initialisation step of the brick.

The main objective of this method is to produce the outputs of the bricks (self.outputs) and the associated tags (self.inheritance_dic), if defined here. In order not to include an output in the database, this output must be a value of the optional key ‘notInDb’ of the self.outputs dictionary. To work properly this method must return self.make_initResult() object.

Parameters:

  • is_plugged – the state, linked or not, of the plugs.

  • iteration – the state, iterative or not, of the process.

Returns:

a dictionary with requirement, outputs and inheritance_dict.

run_process_mia()[source]

Dedicated to the process launch step of the brick.

class mia_processes.bricks.preprocess.ants.processes.Registration[source]

Bases: ProcessMIA

Registers a moving image to a fixed image

Please, see the complete documentation for the Registration brick in the mia_processes website <https://populse.github.io/mia_processes/html/documentation/bricks/preprocess/ants/Registration.html>

Here can be found some of classical registration parameters (used in fMRIPrep and MRIQC) https://github.com/nipreps/niworkflows/tree/master/niworkflows/data

Note

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

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

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

__init__()[source]

Dedicated to the attributes initialisation/instantiation.

The input and output plugs are defined here. The special ‘self.requirement’ attribute (optional) is used to define the third-party products necessary for the running of the brick.

list_outputs(is_plugged=None, iteration=False)[source]

Dedicated to the initialisation step of the brick.

The main objective of this method is to produce the outputs of the bricks (self.outputs) and the associated tags (self.inheritance_dic), if defined here. In order not to include an output in the database, this output must be a value of the optional key ‘notInDb’ of the self.outputs dictionary. To work properly this method must return self.make_initResult() object.

Parameters:

  • is_plugged – the state, linked or not, of the plugs.

  • iteration – the state, iterative or not, of the process.

Returns:

a dictionary with requirement, outputs and inheritance_dict.

run_process_mia()[source]

Dedicated to the process launch step of the brick.