.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.spm.utils
====================


.. _nipype.interfaces.spm.utils.Analyze2nii:


.. index:: Analyze2nii

Analyze2nii
-----------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/spm/utils.py#L19>`__

Inputs::

        [Mandatory]
        analyze_file: (an existing file name)

        [Optional]
        analyze_file: (an existing file name)
        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

.. _nipype.interfaces.spm.utils.ApplyInverseDeformation:


.. index:: ApplyInverseDeformation

ApplyInverseDeformation
-----------------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/spm/utils.py#L251>`__

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

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

.. _nipype.interfaces.spm.utils.ApplyTransform:


.. index:: ApplyTransform

ApplyTransform
--------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/spm/utils.py#L130>`__

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() # doctest: +SKIP

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

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

.. _nipype.interfaces.spm.utils.CalcCoregAffine:


.. index:: CalcCoregAffine

CalcCoregAffine
---------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/spm/utils.py#L53>`__

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

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
        moving: (an existing file name)
                volume transform can be applied to register with target
        paths: (a directory name)
                Paths to add to matlabpath
        target: (an existing file name)
                target for generating affine transform
        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

.. _nipype.interfaces.spm.utils.DicomImport:


.. index:: DicomImport

DicomImport
-----------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/spm/utils.py#L395>`__

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

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

.. _nipype.interfaces.spm.utils.Reslice:


.. index:: Reslice

Reslice
-------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/spm/utils.py#L183>`__

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

.. _nipype.interfaces.spm.utils.ResliceToReference:


.. index:: ResliceToReference

ResliceToReference
------------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/spm/utils.py#L323>`__

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

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