nipype.interfaces.spm.utils module

Analyze2nii

Link to code

Bases: SPMCommand

analyze_file : a pathlike object or string representing an existing file

matlab_cmd : a unicode string
Matlab command to use.
mfile : a boolean
Run m-code using m-file. (Nipype default value: True)
paths : a list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
use_mcr : a boolean
Run m-code using SPM MCR.
use_v8struct : a boolean
Generate SPM8 and higher compatible jobs. (Nipype default value: True)
matlab_cmd : a unicode string
Matlab command to use.
mfile : a boolean
Run m-code using m-file. (Nipype default value: True)

nifti_file : a pathlike object or string representing an existing file paths : a list of items which are a pathlike object or string representing a directory

Paths to add to matlabpath.
use_mcr : a boolean
Run m-code using SPM MCR.
use_v8struct : a boolean
Generate SPM8 and higher compatible jobs. (Nipype default value: True)

ApplyInverseDeformation

Link to code

Bases: SPMCommand

Uses spm to apply inverse deformation stored in a .mat file or a deformation field to a given file

Examples

>>> import nipype.interfaces.spm.utils as spmu
>>> inv = spmu.ApplyInverseDeformation()
>>> inv.inputs.in_files = 'functional.nii'
>>> inv.inputs.deformation = 'struct_to_func.mat'
>>> inv.inputs.target = 'structural.nii'
>>> inv.run() # doctest: +SKIP
in_files : a list of items which are a pathlike object or string representing an existing file
Files on which deformation is applied.
bounding_box : a list of from 6 to 6 items which are a float
6-element list (opt).
deformation : a pathlike object or string representing an existing file
SN SPM deformation file. Mutually exclusive with inputs: deformation_field.
deformation_field : a pathlike object or string representing an existing file
SN SPM deformation file. Mutually exclusive with inputs: deformation.
interpolation : 0 <= a long integer <= 7
Degree of b-spline used for interpolation.
matlab_cmd : a unicode string
Matlab command to use.
mfile : a boolean
Run m-code using m-file. (Nipype default value: True)
paths : a list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
target : a pathlike object or string representing an existing file
File defining target space.
use_mcr : a boolean
Run m-code using SPM MCR.
use_v8struct : a boolean
Generate SPM8 and higher compatible jobs. (Nipype default value: True)
voxel_sizes : a list of from 3 to 3 items which are a float
3-element list (opt).
out_files : a list of items which are a pathlike object or string representing an existing file
Transformed files.

ApplyTransform

Link to code

Bases: SPMCommand

Uses SPM to apply transform stored in a .mat file to given file

Examples

>>> import nipype.interfaces.spm.utils as spmu
>>> applymat = spmu.ApplyTransform()
>>> applymat.inputs.in_file = 'functional.nii'
>>> applymat.inputs.mat = 'func_to_struct.mat'
>>> applymat.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
File to apply transform to, (only updates header).
mat : a pathlike object or string representing an existing file
File holding transform to apply.
matlab_cmd : a unicode string
Matlab command to use.
mfile : a boolean
Run m-code using m-file. (Nipype default value: True)
out_file : a pathlike object or string representing a file
Output file name for transformed data.
paths : a list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
use_mcr : a boolean
Run m-code using SPM MCR.
use_v8struct : a boolean
Generate SPM8 and higher compatible jobs. (Nipype default value: True)
out_file : a pathlike object or string representing an existing file
Transformed image file.

CalcCoregAffine

Link to code

Bases: SPMCommand

Uses SPM (spm_coreg) to calculate the transform mapping moving to target. Saves Transform in mat (matlab binary file) Also saves inverse transform

Examples

>>> import nipype.interfaces.spm.utils as spmu
>>> coreg = spmu.CalcCoregAffine(matlab_cmd='matlab-spm8')
>>> coreg.inputs.target = 'structural.nii'
>>> coreg.inputs.moving = 'functional.nii'
>>> coreg.inputs.mat = 'func_to_struct.mat'
>>> coreg.run() # doctest: +SKIP

Note

  • the output file mat is saves as a matlab binary file
  • calculating the transforms does NOT change either input image it does not move the moving image, only calculates the transform that can be used to move it
moving : a pathlike object or string representing an existing file
Volume transform can be applied to register with target.
target : a pathlike object or string representing an existing file
Target for generating affine transform.
invmat : a pathlike object or string representing a file
Filename used to store inverse affine matrix.
mat : a pathlike object or string representing a file
Filename used to store affine matrix.
matlab_cmd : a unicode string
Matlab command to use.
mfile : a boolean
Run m-code using m-file. (Nipype default value: True)
paths : a list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
use_mcr : a boolean
Run m-code using SPM MCR.
use_v8struct : a boolean
Generate SPM8 and higher compatible jobs. (Nipype default value: True)
invmat : a pathlike object or string representing a file
Matlab file holding inverse transform.
mat : a pathlike object or string representing an existing file
Matlab file holding transform.

DicomImport

Link to code

Bases: SPMCommand

Uses spm to convert DICOM files to nii or img+hdr.

Examples

>>> import nipype.interfaces.spm.utils as spmu
>>> di = spmu.DicomImport()
>>> di.inputs.in_files = ['functional_1.dcm', 'functional_2.dcm']
>>> di.run() # doctest: +SKIP
in_files : a list of items which are a pathlike object or string representing an existing file
Dicom files to be converted.
format : ‘nii’ or ‘img’
Output format. (Nipype default value: nii)
icedims : a boolean
If image sorting fails, one can try using the additional SIEMENS ICEDims information to create unique filenames. Use this only if there would be multiple volumes with exactly the same file names. (Nipype default value: False)
matlab_cmd : a unicode string
Matlab command to use.
mfile : a boolean
Run m-code using m-file. (Nipype default value: True)
output_dir : a unicode string
Output directory. (Nipype default value: ./converted_dicom)
output_dir_struct : ‘flat’ or ‘series’ or ‘patname’ or ‘patid_date’ or ‘patid’ or ‘date_time’
Directory structure for the output. (Nipype default value: flat)
paths : a list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
use_mcr : a boolean
Run m-code using SPM MCR.
use_v8struct : a boolean
Generate SPM8 and higher compatible jobs. (Nipype default value: True)
out_files : a list of items which are a pathlike object or string representing an existing file
Converted files.

Reslice

Link to code

Bases: SPMCommand

uses spm_reslice to resample in_file into space of space_defining

in_file : a pathlike object or string representing an existing file
File to apply transform to, (only updates header).
space_defining : a pathlike object or string representing an existing file
Volume defining space to slice in_file into.
interp : 0 <= a long integer <= 7
Degree of b-spline used for interpolation0 is nearest neighbor (default). (Nipype default value: 0)
matlab_cmd : a unicode string
Matlab command to use.
mfile : a boolean
Run m-code using m-file. (Nipype default value: True)
out_file : a pathlike object or string representing a file
Optional file to save resliced volume.
paths : a list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
use_mcr : a boolean
Run m-code using SPM MCR.
use_v8struct : a boolean
Generate SPM8 and higher compatible jobs. (Nipype default value: True)
out_file : a pathlike object or string representing an existing file
Resliced volume.

ResliceToReference

Link to code

Bases: SPMCommand

Uses spm to reslice a volume to a target image space or to a provided voxel size and bounding box

Examples

>>> import nipype.interfaces.spm.utils as spmu
>>> r2ref = spmu.ResliceToReference()
>>> r2ref.inputs.in_files = 'functional.nii'
>>> r2ref.inputs.target = 'structural.nii'
>>> r2ref.run() # doctest: +SKIP
in_files : a list of items which are a pathlike object or string representing an existing file
Files on which deformation is applied.
bounding_box : a list of from 6 to 6 items which are a float
6-element list (opt).
interpolation : 0 <= a long integer <= 7
Degree of b-spline used for interpolation.
matlab_cmd : a unicode string
Matlab command to use.
mfile : a boolean
Run m-code using m-file. (Nipype default value: True)
paths : a list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
target : a pathlike object or string representing an existing file
File defining target space.
use_mcr : a boolean
Run m-code using SPM MCR.
use_v8struct : a boolean
Generate SPM8 and higher compatible jobs. (Nipype default value: True)
voxel_sizes : a list of from 3 to 3 items which are a float
3-element list (opt).
out_files : a list of items which are a pathlike object or string representing an existing file
Transformed files.