nipype.interfaces.freesurfer.base module

The freesurfer module provides basic functions for interfacing with freesurfer tools.

Currently these tools are supported:

  • Dicom2Nifti: using mri_convert

  • Resample: using mri_convert

Examples

See the docstrings for the individual classes for ‘working’ examples.

FSCommand

Link to code

Bases: CommandLine

General support for FreeSurfer commands.

Every FS command accepts ‘subjects_dir’ input.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

FSCommand.run(**inputs)

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:

  • cwd (specify a folder where the interface should be run)

  • inputs (allows the interface settings to be updated)

Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results

Return type:

nipype.interfaces.base.support.InterfaceResult

classmethod FSCommand.set_default_subjects_dir(subjects_dir)
property FSCommand.version

interfaces should implement a version property

FSCommandOpenMP

Link to code

Bases: FSCommand

Support for FS commands that utilize OpenMP

Sets the environment variable ‘OMP_NUM_THREADS’ to the number of threads specified by the input num_threads.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • num_threads (an integer) – Allows for specifying more threads.

  • subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

FSCommandOpenMP.run(**inputs)

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:

  • cwd (specify a folder where the interface should be run)

  • inputs (allows the interface settings to be updated)

Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results

Return type:

nipype.interfaces.base.support.InterfaceResult

FSScriptCommand

Link to code

Bases: FSCommand

Support for Freesurfer script commands with log terminal_output

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

FSSurfaceCommand

Link to code

Bases: FSCommand

Support for FreeSurfer surface-related functions. For some functions, if the output file is not specified starting with ‘lh.’ or ‘rh.’, FreeSurfer prepends the prefix from the input file to the output filename. Output out_file must be adjusted to accommodate this. By including the full path in the filename, we can also avoid this behavior.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

class nipype.interfaces.freesurfer.base.Info

Bases: nipype.interfaces.base.core.PackageInfo

Freesurfer subject directory and version information.

Examples

>>> from nipype.interfaces.freesurfer import Info
>>> Info.version()  
>>> Info.subjectsdir()
classmethod looseversion()

Return a comparable version object

If no version found, use LooseVersion(‘0.0.0’)

static parse_version(raw_info)
classmethod subjectsdir()

Check the global SUBJECTS_DIR

Parameters:

subjects_dir (string) – The system defined subjects directory

Returns:

subject_dir – Represents the current environment setting of SUBJECTS_DIR

Return type:

string

nipype.interfaces.freesurfer.base.no_freesurfer()

Checks if FreeSurfer is NOT installed used with skipif to skip tests that will fail if FreeSurfer is not installed