interfaces.freesurfer¶

Module: `interfaces.freesurfer`¶

Inheritance diagram for nipype.interfaces.freesurfer:

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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.

Classes¶

`ApplyVolTransform`¶

class nipype.interfaces.freesurfer.ApplyVolTransform(*args, **inputs)¶

Bases: nipype.interfaces.fsl.FSLCommand

Use FreeSurfer mri_vol2vol to apply a transform.

Parameters:

Parameters:	To see optional arguments : ApplyVolTransform().inputs_help() :

To see optional arguments :

ApplyVolTransform().inputs_help() :

Examples

>>> from nipype.interfaces.freesurfer import ApplyVolTransform
>>> applyreg = ApplyVolTransform(tkreg='me.dat', sourcefile='foo.nii',                                      fstarg=True)
>>> applyreg.cmdline
'mri_vol2vol --fstarg --mov foo.nii --reg me.dat --o foo_warped.nii'

__init__(*args, **inputs)¶

aggregate_outputs()¶

cmd¶: sets base command, not editable

cmdline¶: validates fsl options and generates command line argument

get_input_info()¶: Provides information about inputs as a dict info = [Bunch(key=string,copy=bool,ext=’.nii’),...]

inputs_help()¶: Print command line documentation for mri_vol2vol.

outputs()¶

outfile: filename: Warped source file

outputs_help()¶: Print outputs help

run(**inputs)¶: Execute the command.

`BBRegister`¶

class nipype.interfaces.freesurfer.BBRegister(*args, **inputs)¶

Bases: nipype.interfaces.fsl.FSLCommand

Use FreeSurfer bbregister to register a volume two a surface mesh

This program performs within-subject, cross-modal registration using a boundary-based cost function. The registration is constrained to be 6 DOF (rigid). It is required that you have an anatomical scan of the subject that has been analyzed in freesurfer.

Parameters:

Parameters:	To see optional arguments : BBRegister().inputs_help() :

To see optional arguments :

BBRegister().inputs_help() :

Examples

>>> from nipype.interfaces.freesurfer import BBRegister
>>> bbreg = BBRegister(subject_id='me', sourcefile='foo.nii',                            init_header=True, t2_contrast=True)
>>> bbreg.cmdline
'bbregister --init-header --mov foo.nii --s me --t2 --reg foo_bbreg_me.dat'

__init__(*args, **inputs)¶

aggregate_outputs()¶

cmd¶: sets base command, not editable

cmdline¶: validates fsl options and generates command line argument

get_input_info()¶: Provides information about inputs as a dict info = [Bunch(key=string,copy=bool,ext=’.nii’),...]

inputs_help()¶: Print command line documentation for bbregister.

outputs()¶

outregfile: filename: Output registration file
outfile: filename: Registered and resampled source file

outputs_help()¶: Print outputs help

run(**inputs)¶: Execute the command.

`Dicom2Nifti`¶

class nipype.interfaces.freesurfer.Dicom2Nifti¶

Bases: nipype.interfaces.freesurfer.FSCommandLine

use fs mri_convert to convert dicom files to nifti-1 files

Parameters:

Parameters:	To see optional arguments : Dicom2Nifti().inputs_help() :

To see optional arguments :

Dicom2Nifti().inputs_help() :

Examples

>>> from nipype.interfaces import freesurfer
>>> cvt = freesurfer.Dicom2Nifti()
>>> cvt.inputs.dicomdir = '/software/data/STUT/RAWDATA/TrioTim-35115-20090428-081900-234000/'
>>> cvt.inputs.file_mapping = [('nifti','*.nii'),('info','dicom*.txt'),('dti','*dti.bv*')]
>>> #out = cvt.run() # commented out as above directories are not installed

__init__()¶

aggregate_outputs()¶

cmd¶: sets base command, not editable

cmdline¶

get_input_info()¶

Provides information about file inputs to copy or link to cwd.

Notes

see spm.Realign.get_input_info

inputs_help()¶

Parameters:

Parameters:	(all default to None and are unset) : dicomdir : /path/to/dicomfiles directory from which to convert dicom files base_output_dir : /path/to/outputdir base output directory in which subject specific directories are created to store the nifti files subject_dir_template : string template for subject directory name Default:’S.%04d’ subject_id : string or int subject identifier to insert into template. For the example above template subject_identifier should be an integer. Default: id from Dicom file name file_mapping : list of tuples defines the output fields of interface and the kind of file type they store Example: [(‘niftifiles’,’.nii’),(‘dtiinfo’,’mghdti.bv‘)] flags = unsupported flags, use at your own risk* :

(all default to None and are unset) :

dicomdir : /path/to/dicomfiles

directory from which to convert dicom files

base_output_dir : /path/to/outputdir

base output directory in which subject specific directories are created to store the nifti files

subject_dir_template : string

template for subject directory name Default:’S.%04d’

subject_id : string or int

subject identifier to insert into template. For the example above template subject_identifier should be an integer. Default: id from Dicom file name

file_mapping : list of tuples

defines the output fields of interface and the kind of file type they store Example: [(‘niftifiles’,’.nii’),(‘dtiinfo’,’*mghdti.bv‘)]

flags = unsupported flags, use at your own risk :

run(**inputs)¶

Execute the command.

Returns:

Returns:	results : InterfaceResult A InterfaceResult object with a copy of self in interface

results : InterfaceResult

A InterfaceResult object with a copy of self in interface

`FSCommandLine`¶

class nipype.interfaces.freesurfer.FSCommandLine¶

Bases: nipype.interfaces.base.CommandLine

__init__()¶

aggregate_outputs()¶

Called to populate outputs

Currently, search for discussion of this on private e-mails between Dav and Satra (ugh!). This needs to get in here!

cmdline¶

get_input_info()¶

Provides information about file inputs to copy or link to cwd.

Notes

see spm.Realign.get_input_info

run(**inputs)¶

Execute the command.

Returns:

Returns:	results : InterfaceResult A InterfaceResult object with a copy of self in interface

results : InterfaceResult

A InterfaceResult object with a copy of self in interface

`OneSampleTTest`¶

class nipype.interfaces.freesurfer.OneSampleTTest(*args, **inputs)¶

Bases: nipype.interfaces.fsl.FSLCommand

Use FreeSurfer mri_glmfit to prepare a group of contrasts for a second level analysis

Parameters:

Parameters:	To see optional arguments : SurfConcat().inputs_help() :

To see optional arguments :

SurfConcat().inputs_help() :

__init__(*args, **inputs)¶

aggregate_outputs()¶

cmd¶: sets base command, not editable

cmdline¶: validates fsl options and generates command line argument

get_input_info()¶: Provides information about inputs as a dict info = [Bunch(key=string,copy=bool,ext=’.nii’),...]

inputs_help()¶: Print command line documentation for mris_preproc.

outputs()¶

outputs_help()¶: Print outputs help

run(cwd=None, **inputs)¶: Execute the command.

`ReconAll`¶

class nipype.interfaces.freesurfer.ReconAll¶

Bases: nipype.interfaces.freesurfer.FSCommandLine

Use FreeSurfer recon-all to generate surfaces and parcellations of structural data from an anatomical image of a subject.

Parameters:

Parameters:	To see optional arguments : ReconAll().inputs_help() :

To see optional arguments :

ReconAll().inputs_help() :

Examples

>>> from nipype.interfaces import freesurfer
>>> reconall = freesurfer.ReconAll()
>>> reconall.inputs.subject_id = 'foo'
>>> reconall.inputs.directive  = '-all'
>>> reconall.inputs.parent_dir = '.'
>>> reconall.inputs.T1files = 'structfile.nii'
>>> out = reconall.run() # doctest +SKIP

__init__()¶

aggregate_outputs()¶

cmd¶: sets base command, not editable

cmdline¶

get_input_info()¶

Provides information about file inputs to copy or link to cwd.

Notes

see spm.Realign.get_input_info

inputs_help()¶

Parameters:

Parameters:	(all default to None and are unset) : T1files: filename(s) : T1 file or list of files to extract surfaces from. The T1 files must come from the same subject hemi: string : just do lh or rh (default is to do both) parent_dir: string : defaults to SUBJECTS_DIR environment variable. If the variable is not set, it defaults to current working directory. test: : Do everything but execute each command flags: : unsupported flags, use at your own risk

(all default to None and are unset) :

T1files: filename(s) :

T1 file or list of files to extract surfaces from. The T1 files must come from the same subject

hemi: string :

just do lh or rh (default is to do both)

parent_dir: string :

defaults to SUBJECTS_DIR environment variable. If the variable is not set, it defaults to current working directory.

test: :

Do everything but execute each command

flags: :

unsupported flags, use at your own risk

outputs_help()¶: No outputs

run(**inputs)¶

Execute the command.

Returns:

Returns:	results : InterfaceResult A InterfaceResult object with a copy of self in interface

results : InterfaceResult

A InterfaceResult object with a copy of self in interface

`Resample`¶

class nipype.interfaces.freesurfer.Resample¶

Bases: nipype.interfaces.freesurfer.FSCommandLine

Use FreeSurfer mri_convert to up or down-sample image files

Parameters:

Parameters:	To see optional arguments : Resample().inputs_help() :

To see optional arguments :

Resample().inputs_help() :

Examples

>>> from nipype.interfaces import freesurfer
>>> resampler = freesurfer.Resample()
>>> resampler.inputs.infile = 'infile.nii'
>>> resampler.inputs.voxel_size = [2, 2, 2]
>>> out = resampler.run()

__init__()¶

aggregate_outputs()¶

cmd¶: sets base command, not editable

cmdline¶

get_input_info()¶

Provides information about file inputs to copy or link to cwd.

Notes

see spm.Realign.get_input_info

inputs_help()¶

Parameters:

Parameters:	(all default to None and are unset) : infile : string or list file(s) to resample voxel_size: 3-element list : size of x, y and z voxels in mm of resampled image outfile_postfix : string string appended to input file name to generate output file name. Default: ‘_fsresample’ flags = unsupported flags, use at your own risk :

(all default to None and are unset) :

infile : string or list

file(s) to resample

voxel_size: 3-element list :

size of x, y and z voxels in mm of resampled image

outfile_postfix : string

string appended to input file name to generate output file name. Default: ‘_fsresample’

flags = unsupported flags, use at your own risk :

outputs_help()¶

outfile : string or list: resampled file(s)

run(**inputs)¶

Execute the command.

Returns:

Returns:	results : InterfaceResult A InterfaceResult object with a copy of self in interface

results : InterfaceResult

A InterfaceResult object with a copy of self in interface

`Smooth`¶

class nipype.interfaces.freesurfer.Smooth(*args, **inputs)¶

Bases: nipype.interfaces.fsl.FSLCommand

Use FreeSurfer mris_volsmooth to smooth a volume

This function smoothes cortical regions on a surface and non-cortical regions in volume.

Parameters:

Parameters:	To see optional arguments : Smooth().inputs_help() :

To see optional arguments :

Smooth().inputs_help() :

Examples

>>> from nipype.interfaces.freesurfer import Smooth
>>> smoothvol = Smooth(sourcefile='foo.nii', regfile='reg.dat',                            surface_fwhm=10, vol_fwhm=6)
>>> smoothvol.cmdline
'mris_volsmooth --reg reg.dat --i foo.nii --fwhm 10 --vol-fwhm 6 --o foo_surfsmooth.nii'

__init__(*args, **inputs)¶

aggregate_outputs()¶

cmd¶: sets base command, not editable

cmdline¶: validates fsl options and generates command line argument

get_input_info()¶: Provides information about inputs as a dict info = [Bunch(key=string,copy=bool,ext=’.nii’),...]

inputs_help()¶: Print command line documentation for mris_volsmooth.

outputs()¶

outfile: filename: Smoothed input volume

outputs_help()¶: Print outputs help

run(**inputs)¶: Execute the command.

`SurfConcat`¶

class nipype.interfaces.freesurfer.SurfConcat(*args, **inputs)¶

Bases: nipype.interfaces.fsl.FSLCommand

Use FreeSurfer mris_preproc to prepare a group of contrasts for a second level analysis

Parameters:

Parameters:	To see optional arguments : SurfConcat().inputs_help() :

To see optional arguments :

SurfConcat().inputs_help() :

__init__(*args, **inputs)¶

aggregate_outputs()¶

cmd¶: sets base command, not editable

cmdline¶: validates fsl options and generates command line argument

get_input_info()¶: Provides information about inputs as a dict info = [Bunch(key=string,copy=bool,ext=’.nii’),...]

inputs_help()¶: Print command line documentation for mris_preproc.

outputs()¶

outfile: filename: Concatenated volume

outputs_help()¶: Print outputs help

run(**inputs)¶: Execute the command.

Functions¶

nipype.interfaces.freesurfer.freesurferversion()¶

Check for freesurfer version on system

Parameters:

Parameters:	None :
Returns:	version : string version number as string or None if freesurfer version not found

None :

Returns:

version : string

version number as string or None if freesurfer version not found

nipype.interfaces.freesurfer.fssubjectsdir(subjects_dir=None)¶

Check and or set the global SUBJECTS_DIR

Parameters:

Parameters:	subjects_dir : string The system defined subjects directory
Returns:	subject_dir : string Represents the current environment setting of SUBJECTS_DIR

subjects_dir : string

The system defined subjects directory

Returns:

subject_dir : string

Represents the current environment setting of SUBJECTS_DIR

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interfaces.freesurfer¶

Module: `interfaces.freesurfer`¶

Examples¶

Classes¶

`ApplyVolTransform`¶

`BBRegister`¶

`Dicom2Nifti`¶

`FSCommandLine`¶

`OneSampleTTest`¶

`ReconAll`¶

`Resample`¶

`Smooth`¶

`SurfConcat`¶

Functions¶

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interfaces.freesurfer¶

Module: interfaces.freesurfer¶

Examples¶

Classes¶

Functions¶

Module: `interfaces.freesurfer`¶