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interfaces.spm.utils

Analyze2nii

Link to code

Inputs:

[Mandatory]
analyze_file: (an existing file name)

[Optional]
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
matlab_cmd: (a string)
        matlab command to use
mfile: (a boolean, nipype default value: True)
        Run m-code using m-file
paths: (a directory name)
        Paths to add to matlabpath
use_mcr: (a boolean)
        Run m-code using SPM MCR

Outputs:

ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
matlab_cmd: (a string)
        matlab command to use
mfile: (a boolean, nipype default value: True)
        Run m-code using m-file
nifti_file: (an existing file name)
paths: (a directory name)
        Paths to add to matlabpath
use_mcr: (a boolean)
        Run m-code using SPM MCR

ApplyTransform

Link to code

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

Examples

>>> import nipype.interfaces.spm.utils as spmu
>>> applymat = spmu.ApplyTransform(matlab_cmd='matlab-spm8')
>>> applymat.inputs.in_file = 'functional.nii'
>>> applymat.inputs.mat = 'func_to_struct.mat'
>>> applymat.run() 

Warning

CHANGES YOUR INPUT FILE (applies transform by updating the header) except when used with nipype caching or workflow.

Inputs:

[Mandatory]
in_file: (an existing file name)
        file to apply transform to, (only updates header)
mat: (an existing file name)
        file holding transform to apply

[Optional]
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
matlab_cmd: (a string)
        matlab command to use
mfile: (a boolean, nipype default value: True)
        Run m-code using m-file
paths: (a directory name)
        Paths to add to matlabpath
use_mcr: (a boolean)
        Run m-code using SPM MCR

Outputs:

out_file: (an existing file name)
        File with updated header

CalcCoregAffine

Link to code

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() 

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

Inputs:

[Mandatory]
moving: (an existing file name)
        volume transform can be applied to register with target
target: (an existing file name)
        target for generating affine transform

[Optional]
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
invmat: (a file name)
        Filename used to store inverse affine matrix
mat: (a file name)
        Filename used to store affine matrix
matlab_cmd: (a string)
        matlab command to use
mfile: (a boolean, nipype default value: True)
        Run m-code using m-file
paths: (a directory name)
        Paths to add to matlabpath
use_mcr: (a boolean)
        Run m-code using SPM MCR

Outputs:

invmat: (a file name)
        Matlab file holding inverse transform
mat: (an existing file name)
        Matlab file holding transform

Reslice

Link to code

uses spm_reslice to resample in_file into space of space_defining

Inputs:

[Mandatory]
in_file: (an existing file name)
        file to apply transform to, (only updates header)
space_defining: (an existing file name)
        Volume defining space to slice in_file into

[Optional]
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
interp: (0 <= an integer <= 7, nipype default value: 0)
        degree of b-spline used for interpolation0 is nearest neighbor (default)
matlab_cmd: (a string)
        matlab command to use
mfile: (a boolean, nipype default value: True)
        Run m-code using m-file
out_file: (a file name)
        Optional file to save resliced volume
paths: (a directory name)
        Paths to add to matlabpath
use_mcr: (a boolean)
        Run m-code using SPM MCR

Outputs:

out_file: (an existing file name)
        resliced volume