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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

## ApplyInverseDeformation

Link to code

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()

Inputs:

    [Mandatory]
    in_files: (an existing file name)
            Files on which deformation is applied

    [Optional]
    bounding_box: (a list of from 6 to 6 items which are a float)
            6-element list (opt)
    deformation: (an existing file name)
            SN SPM deformation file
            mutually_exclusive: deformation_field
    deformation_field: (an existing file name)
            SN SPM deformation file
            mutually_exclusive: deformation
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the interface fails to
            run
    interpolation: (an integer >= 0)
            degree of b-spline used for interpolation
    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
    target: (an existing file name)
            File defining target space
    use_mcr: (a boolean)
            Run m-code using SPM MCR
    voxel_sizes: (a list of from 3 to 3 items which are a float)
            3-element list (opt)

Outputs:

    out_files: (an existing file name)
            Transformed files

## 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