mia_processes.bricks.preprocess.fsl package

The atomic calculations from fsl.

Submodules

mia_processes.bricks.preprocess.fsl.processes module

The fsl preprocess library of the mia_processes package.

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

Contains:
Class:

  • Bet

  • BetSurfacesExtraction

  • ConvertXFM

  • EpiReg

  • ExtractROI

  • FastSegment

  • Flirt

  • Smooth

class mia_processes.bricks.preprocess.fsl.processes.Bet[source]

Bases: ProcessMIA

Use BET (FSL)

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

Note

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

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

  • Type ‘<Bet>.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.fsl.processes.BetSurfacesExtraction[source]

Bases: ProcessMIA

Surfaces (skull, inskull, outskull, outskin) extraction using BET (FSL)

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

Note

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

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

  • Type ‘<BetSurfacesExtraction>.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.fsl.processes.ConvertXFM[source]

Bases: ProcessMIA

Modify transformation matrice using convert_xfm (FSL)

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

Note

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

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

  • Type ‘<ConvertXFM>.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.fsl.processes.EpiReg[source]

Bases: ProcessMIA

Run epi_reg script (FSL) to register EPI images to structural images

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

Note

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

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

  • Type ‘<EpiReg>.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.fsl.processes.ExtractROI[source]

Bases: ProcessMIA

Extract region of interest (ROI) from an image using FslROI

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

Note

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

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

  • Type ‘<ExtractROI>.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.fsl.processes.FastSegment[source]

Bases: ProcessMIA

Brain tissue segmentation using fsl.FAST

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

Note

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

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

  • Type ‘<FastSegment>.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.fsl.processes.Flirt[source]

Bases: ProcessMIA

Linear (affine) intra and inter-modal brain image registration using fsl FLIRT

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

Note

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

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

  • Type ‘<Flirt>.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.fsl.processes.Smooth[source]

Bases: ProcessMIA

3D Gaussian smoothing of image volumes

Please, see the complete documentation for the Smooth’ brick in the mia_processes website

Note

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

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

  • Type ‘<Smooth>.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.