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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
    use_v8struct: (a boolean, nipype default value: True)
            Generate SPM8 and higher compatible jobs

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
    use_v8struct: (a boolean, nipype default value: True)
            Generate SPM8 and higher compatible jobs

## 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: (0 <= an integer <= 7)
            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
    use_v8struct: (a boolean, nipype default value: True)
            Generate SPM8 and higher compatible jobs
    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()
    >>> applymat.inputs.in_file = 'functional.nii'
    >>> applymat.inputs.mat = 'func_to_struct.mat'
    >>> applymat.run()

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
    out_file: (a file name)
            output file name for transformed data
    paths: (a directory name)
            Paths to add to matlabpath
    use_mcr: (a boolean)
            Run m-code using SPM MCR
    use_v8struct: (a boolean, nipype default value: True)
            Generate SPM8 and higher compatible jobs

Outputs:

    out_file: (an existing file name)
            Transformed image file

## 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
    use_v8struct: (a boolean, nipype default value: True)
            Generate SPM8 and higher compatible jobs

Outputs:

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

## DicomImport

Link to code

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()

Inputs:

    [Mandatory]
    in_files: (an existing file name)
            dicom files to be converted

    [Optional]
    format: ('nii' or 'img', nipype default value: nii)
            output format.
    icedims: (a boolean, nipype default value: False)
            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.
    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
    output_dir: (a string, nipype default value: ./converted_dicom)
            output directory.
    output_dir_struct: ('flat' or 'series' or 'patname' or 'patid_date'
             or 'patid' or 'date_time', nipype default value: flat)
            directory structure for the output.
    paths: (a directory name)
            Paths to add to matlabpath
    use_mcr: (a boolean)
            Run m-code using SPM MCR
    use_v8struct: (a boolean, nipype default value: True)
            Generate SPM8 and higher compatible jobs

Outputs:

    out_files: (an existing file name)
            converted files

## 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
    use_v8struct: (a boolean, nipype default value: True)
            Generate SPM8 and higher compatible jobs

Outputs:

    out_file: (an existing file name)
            resliced volume

## ResliceToReference

Link to code

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()

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)
    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: (0 <= an integer <= 7)
            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
    use_v8struct: (a boolean, nipype default value: True)
            Generate SPM8 and higher compatible jobs
    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