mia_processes package

Mia_processes is the official bricks library for populse_mia. A brick can be an atomic operation or a pipeline (a succession of atomic calculations).

Contains:

Packages:

• bricks: the library of atomic bricks

• pipelines: the pipelines library

• utils: various general tools used in bricks or pipelines

Subpackages

• mia_processes.bricks package
  • Subpackages
    • mia_processes.bricks.preprocess package
      • Subpackages
    • mia_processes.bricks.reports package
      • Submodules
      • mia_processes.bricks.reports.processes module
      • mia_processes.bricks.reports.reporting module
    • mia_processes.bricks.stat package
      • Subpackages
    • mia_processes.bricks.tools package
      • Submodules
      • mia_processes.bricks.tools.tools module
• mia_processes.pipelines package
  • Subpackages
    • mia_processes.pipelines.CerebVascularReact package
      • Submodules
      • mia_processes.pipelines.CerebVascularReact.co2_inhalation module
    • mia_processes.pipelines.DWITractography package
      • Submodules
      • mia_processes.pipelines.DWITractography.dwi_whole_brain_tractography module
    • mia_processes.pipelines.preprocess package
      • Submodules
      • mia_processes.pipelines.preprocess.anat_airmask module
      • mia_processes.pipelines.preprocess.anat_headmask module
      • mia_processes.pipelines.preprocess.anat_mni_tpms module
      • mia_processes.pipelines.preprocess.anat_skullstrip module
      • mia_processes.pipelines.preprocess.anat_skullstrip_synthstrip module
      • mia_processes.pipelines.preprocess.anat_spatial_norm module
      • mia_processes.pipelines.preprocess.bold_hmc module
      • mia_processes.pipelines.preprocess.bold_mni_align module
      • mia_processes.pipelines.preprocess.bold_spatial_preprocessing1 module
      • mia_processes.pipelines.preprocess.bold_spatial_preprocessing2 module
      • mia_processes.pipelines.preprocess.dwi_fod_msmt_csd module
      • mia_processes.pipelines.preprocess.dwipreprocessing module
      • mia_processes.pipelines.preprocess.spatial_mask module
    • mia_processes.pipelines.qualityControl package
      • Submodules
      • mia_processes.pipelines.qualityControl.anat_mriqc module
      • mia_processes.pipelines.qualityControl.bold_mriqc module
    • mia_processes.pipelines.reports package
      • Submodules
      • mia_processes.pipelines.reports.bold_iqms module
      • mia_processes.pipelines.reports.extract_roi_param module
    • mia_processes.pipelines.stat package
      • Submodules
      • mia_processes.pipelines.stat.bold_stat_cvr module
• mia_processes.utils package
  • Submodules
  • mia_processes.utils.report module
    • Report
      • Report.__init__()
      • Report.co2_inhal_cvr_make_report()
      • Report.ge2rec_make_report()
      • Report.get_iqms_data()
      • Report.mriqc_anat_make_report()
      • Report.mriqc_func_make_report()
      • Report.mriqc_group_make_report()
      • Report.perf_dsc_make_report()
  • mia_processes.utils.tools module
    • PageNumCanvas
      • PageNumCanvas.__init__()
      • PageNumCanvas.draw_page_number()
      • PageNumCanvas.save()
      • PageNumCanvas.showPage()
    • ReportLine
      • ReportLine.__init__()
      • ReportLine.draw()
    • checkFileExt()
    • check_orientations()
    • del_dbFieldValue()
    • dict4runtime_update()
    • get_dbFieldValue()
    • mriqc_get_all_run()
    • mriqc_group_iqms_tsv()
    • plot_boxplot_points()
    • plot_qi2()
    • plot_realignment_parameters()
    • plot_segmentation()
    • plot_slice_planes()
    • set_dbFieldValue()

Submodules

mia_processes.info module

The module dedicated to the main information on mia_processes.

The info.py module is mainly used by the setup.py module.

mia_processes.info.get_gitversion()

Mia_processes version as reported by the last commit in git Returns the version or None if nothing was found

mia_processes.process_matlab module

The toobox to run a brick using Matlab.

Basically, this module provides the necessary tools for the launch of the bricks using Matlab.

Contains:

Class:

• ProcessMatlab

class mia_processes.process_matlab.ProcessMatlab

Bases: ProcessMIA

Class overriding the ProcessMIA class, in order to use Matlab.

Note

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

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

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

__init__()

Initialize the Process class.

add_exit()

Adds an exit to the Matlab script.

add_path(path)

Adds a Matlab path to the Matlab script.

Parameters:

path – Matlab path

change_directory(directory)

Changes the working directory in the Matlab script.

Parameters:

directory – directory

display_parameter(parameter_name)

Displays a given parameter in the Matlab script.

Parameters:

parameter_name – name of the parameter

run()

Runs the Matlab script.

set_global_variable(variable_name)

Adds a global variable to the Matlab script.

Parameters:

variable_name – name of the variable

set_variable(variable_name, value)

Assign a value to a variable in the Matlab script.

Parameters:

• variable_name – name of the variable

• value – value of the variable