mia_processes.bricks.preprocess.spm package

The atomic calculations from spm.

Submodules

mia_processes.bricks.preprocess.spm.spatial_preprocessing module

The spm preprocess library of the mia_processes package.

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

Contains:
Class:

  • Coregister

  • GM_WM_Normalize

  • NewSegment

  • Normalize12

  • Realign

  • SliceTiming

  • Smooth

class mia_processes.bricks.preprocess.spm.spatial_preprocessing.Coregister[source]

Bases: ProcessMIA

Align together scans of different modalities

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

Note

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

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

  • Type ‘<Coregister>.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.spm.spatial_preprocessing.GM_WM_Normalize[source]

Bases: ProcessMIA

Normalisation of the grey and/or white matter map(s)

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

Note

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

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

  • Type ‘<GM_WM_Normalize>.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.spm.spatial_preprocessing.NewSegment[source]

Bases: ProcessMIA

Segmentation: Segments, bias corrects and spatially normalises

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

Note

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

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

  • Type ‘<NewSegment>.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.spm.spatial_preprocessing.Normalize12[source]

Bases: ProcessMIA

Computes the warp that best aligns the template (atlas) to the image

Please, see the complete documentation for the Normalize12 brick in the mia_processes website

Note

  • Type ‘Normalize12.help()’ for a full description of this process parameters.

  • Type ‘<Normalize12>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Normalize12>.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.spm.spatial_preprocessing.Realign[source]

Bases: ProcessMIA

Realigns a time-series of images acquired from the same subject

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

Note

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

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

  • Type ‘<Realign>.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.spm.spatial_preprocessing.SliceTiming[source]

Bases: ProcessMIA

Temporal correction to get back every slice at the same acquisition time

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

Note

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

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

  • Type ‘<SliceTiming>.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.spm.spatial_preprocessing.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.