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

interfaces.freesurfer.registration
==================================


.. _nipype.interfaces.freesurfer.registration.EMRegister:


.. index:: EMRegister

EMRegister
----------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/freesurfer/registration.py#L230>`__

Wraps command **mri_em_register**

This program creates a tranform in lta format

Examples
~~~~~~~~
>>> from nipype.interfaces.freesurfer import EMRegister
>>> register = EMRegister()
>>> register.inputs.in_file = 'norm.mgz'
>>> register.inputs.template = 'aseg.mgz'
>>> register.inputs.out_file = 'norm_transform.lta'
>>> register.inputs.skull = True
>>> register.inputs.nbrspacing = 9
>>> register.cmdline
'mri_em_register -uns 9 -skull norm.mgz aseg.mgz norm_transform.lta'

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                in brain volume
                flag: %s, position: -3
        template: (an existing file name)
                template gca
                flag: %s, position: -2

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %s
        environ: (a dictionary with keys which are a newbytes or None or a
                 newstr or None and with values which are a newbytes or None or a
                 newstr or None, nipype default value: {})
                Environment variables
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        mask: (an existing file name)
                use volume as a mask
                flag: -mask %s
        nbrspacing: (an integer (int or long))
                align to atlas containing skull setting unknown_nbr_spacing =
                nbrspacing
                flag: -uns %d
        num_threads: (an integer (int or long))
                allows for specifying more threads
        out_file: (a file name)
                output transform
                flag: %s, position: -1
        skull: (a boolean)
                align to atlas containing skull (uns=5)
                flag: -skull
        subjects_dir: (an existing directory name)
                subjects directory
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
                Control terminal output: `stream` - displays to terminal immediately
                (default), `allatonce` - waits till command is finished to display
                output, `file` - writes output to file, `none` - output is ignored
        transform: (an existing file name)
                Previously computed transform
                flag: -t %s

Outputs::

        out_file: (a file name)
                output transform

.. _nipype.interfaces.freesurfer.registration.MPRtoMNI305:


.. index:: MPRtoMNI305

MPRtoMNI305
-----------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/freesurfer/registration.py#L50>`__

Wraps command **mpr2mni305**

For complete details, see FreeSurfer documentation

Examples
~~~~~~~~

>>> from nipype.interfaces.freesurfer import MPRtoMNI305, Info
>>> mprtomni305 = MPRtoMNI305()
>>> mprtomni305.inputs.target = 'structural.nii'
>>> mprtomni305.inputs.reference_dir = '.' # doctest: +SKIP
>>> mprtomni305.cmdline # doctest: +SKIP
'mpr2mni305 output'
>>> mprtomni305.inputs.out_file = 'struct_out' # doctest: +SKIP
>>> mprtomni305.cmdline # doctest: +SKIP
'mpr2mni305 struct_out' # doctest: +SKIP
>>> mprtomni305.inputs.environ['REFDIR'] == os.path.join(Info.home(), 'average') # doctest: +SKIP
True
>>> mprtomni305.inputs.environ['MPR2MNI305_TARGET'] # doctest: +SKIP
'structural'
>>> mprtomni305.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        reference_dir: (an existing directory name, nipype default value: )
                TODO
        target: (a string, nipype default value: )
                input atlas file

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %s
        environ: (a dictionary with keys which are a newbytes or None or a
                 newstr or None and with values which are a newbytes or None or a
                 newstr or None, nipype default value: {})
                Environment variables
        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: (a file name, nipype default value: )
                the input file prefix for MPRtoMNI305
                flag: %s
        subjects_dir: (an existing directory name)
                subjects directory
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
                Control terminal output: `stream` - displays to terminal immediately
                (default), `allatonce` - waits till command is finished to display
                output, `file` - writes output to file, `none` - output is ignored

Outputs::

        log_file: (an existing file name, nipype default value:
                 output.nipype)
                The output log
        out_file: (a file name)
                The output file '<in_file>_to_<target>_t4_vox2vox.txt'

.. _nipype.interfaces.freesurfer.registration.MRICoreg:


.. index:: MRICoreg

MRICoreg
--------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/freesurfer/registration.py#L545>`__

Wraps command **mri_coreg**

This program registers one volume to another

mri_coreg is a C reimplementation of spm_coreg in FreeSurfer

Examples
~~~~~~~~
>>> from nipype.interfaces.freesurfer import MRICoreg
>>> coreg = MRICoreg()
>>> coreg.inputs.source_file = 'moving1.nii'
>>> coreg.inputs.reference_file = 'fixed1.nii'
>>> coreg.inputs.subjects_dir = '.'
>>> coreg.cmdline # doctest: +ELLIPSIS
'mri_coreg --lta .../registration.lta --ref fixed1.nii --mov moving1.nii --sd .'

If passing a subject ID, the reference mask may be disabled:

>>> coreg = MRICoreg()
>>> coreg.inputs.source_file = 'moving1.nii'
>>> coreg.inputs.subjects_dir = '.'
>>> coreg.inputs.subject_id = 'fsaverage'
>>> coreg.inputs.reference_mask = False
>>> coreg.cmdline # doctest: +ELLIPSIS
'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --mov moving1.nii --sd .'

Spatial scales may be specified as a list of one or two separations:

>>> coreg.inputs.sep = [4]
>>> coreg.cmdline # doctest: +ELLIPSIS
'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --mov moving1.nii --sd .'

>>> coreg.inputs.sep = [4, 5]
>>> coreg.cmdline # doctest: +ELLIPSIS
'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --sep 5 --mov moving1.nii --sd .'

Inputs::

        [Mandatory]
        reference_file: (a file name)
                reference (target) file
                flag: --ref %s
                mutually_exclusive: subject_id
        source_file: (a file name)
                source file to be registered
                flag: --mov %s
        subject_id: (a unicode string)
                freesurfer subject ID (implies ``reference_mask == aparc+aseg.mgz``
                unless otherwise specified)
                flag: --s %s, position: 1
                mutually_exclusive: reference_file
                requires: subjects_dir

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %s
        brute_force_limit: (a float)
                constrain brute force search to +/- lim
                flag: --bf-lim %g
                mutually_exclusive: no_brute_force
        brute_force_samples: (an integer (int or long))
                number of samples in brute force search
                flag: --bf-nsamp %d
                mutually_exclusive: no_brute_force
        conform_reference: (a boolean)
                conform reference without rescaling
                flag: --conf-ref
        dof: (6 or 9 or 12)
                number of transform degrees of freedom
                flag: --dof %d
        environ: (a dictionary with keys which are a newbytes or None or a
                 newstr or None and with values which are a newbytes or None or a
                 newstr or None, nipype default value: {})
                Environment variables
        ftol: (a float)
                floating-point tolerance (default=1e-7)
                flag: --ftol %e
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        initial_rotation: (a tuple of the form: (a float, a float, a float))
                initial rotation in degrees
                flag: --rot %g %g %g
        initial_scale: (a tuple of the form: (a float, a float, a float))
                initial scale
                flag: --scale %g %g %g
        initial_shear: (a tuple of the form: (a float, a float, a float))
                initial shear (Hxy, Hxz, Hyz)
                flag: --shear %g %g %g
        initial_translation: (a tuple of the form: (a float, a float, a
                 float))
                initial translation in mm (implies no_cras0)
                flag: --trans %g %g %g
        linmintol: (a float)
                flag: --linmintol %e
        max_iters: (an integer >= 1)
                maximum iterations (default: 4)
                flag: --nitersmax %d
        no_brute_force: (a boolean)
                do not brute force search
                flag: --no-bf
        no_coord_dithering: (a boolean)
                turn off coordinate dithering
                flag: --no-coord-dither
        no_cras0: (a boolean)
                do not set translation parameters to align centers of source and
                reference files
                flag: --no-cras0
        no_intensity_dithering: (a boolean)
                turn off intensity dithering
                flag: --no-intensity-dither
        no_smooth: (a boolean)
                do not apply smoothing to either reference or source file
                flag: --no-smooth
        num_threads: (an integer (int or long))
                number of OpenMP threads
                flag: --threads %d
        out_lta_file: (a bool or None or a file name, nipype default value:
                 True)
                output registration file (LTA format)
                flag: --lta %s
        out_params_file: (a bool or None or a file name)
                output parameters file
                flag: --params %s
        out_reg_file: (a bool or None or a file name)
                output registration file (REG format)
                flag: --regdat %s
        ref_fwhm: (a float)
                apply smoothing to reference file
                flag: --ref-fwhm
        reference_mask: (a bool or None or a unicode string)
                mask reference volume with given mask, or None if ``False``
                flag: --ref-mask %s, position: 2
        saturation_threshold: (0.0 <= a floating point number <= 100.0)
                saturation threshold (default=9.999)
                flag: --sat %g
        sep: (a list of from 1 to 2 items which are any value)
                set spatial scales, in voxels (default [2, 4])
                flag: --sep %s...
        source_mask: (a unicode string)
                mask source file with given mask
                flag: --mov-mask
        source_oob: (a boolean)
                count source voxels that are out-of-bounds as 0
                flag: --mov-oob
        subjects_dir: (an existing directory name)
                FreeSurfer SUBJECTS_DIR
                flag: --sd %s
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
                Control terminal output: `stream` - displays to terminal immediately
                (default), `allatonce` - waits till command is finished to display
                output, `file` - writes output to file, `none` - output is ignored

Outputs::

        out_lta_file: (an existing file name)
                output LTA-style registration file
        out_params_file: (an existing file name)
                output parameters file
        out_reg_file: (an existing file name)
                output registration file

.. _nipype.interfaces.freesurfer.registration.Paint:


.. index:: Paint

Paint
-----

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/freesurfer/registration.py#L379>`__

Wraps command **mrisp_paint**

This program is useful for extracting one of the arrays ("a variable")
from a surface-registration template file. The output is a file
containing a surface-worth of per-vertex values, saved in "curvature"
format. Because the template data is sampled to a particular surface
mesh, this conjures the idea of "painting to a surface".

Examples
~~~~~~~~
>>> from nipype.interfaces.freesurfer import Paint
>>> paint = Paint()
>>> paint.inputs.in_surf = 'lh.pial'
>>> paint.inputs.template = 'aseg.mgz'
>>> paint.inputs.averages = 5
>>> paint.inputs.out_file = 'lh.avg_curv'
>>> paint.cmdline
'mrisp_paint -a 5 aseg.mgz lh.pial lh.avg_curv'

Inputs::

        [Mandatory]
        in_surf: (an existing file name)
                Surface file with grid (vertices) onto which the template data is to
                be sampled or 'painted'
                flag: %s, position: -2
        template: (an existing file name)
                Template file
                flag: %s, position: -3

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %s
        averages: (an integer (int or long))
                Average curvature patterns
                flag: -a %d
        environ: (a dictionary with keys which are a newbytes or None or a
                 newstr or None and with values which are a newbytes or None or a
                 newstr or None, nipype default value: {})
                Environment variables
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        out_file: (a file name)
                File containing a surface-worth of per-vertex values, saved in
                'curvature' format.
                flag: %s, position: -1
        subjects_dir: (an existing directory name)
                subjects directory
        template_param: (an integer (int or long))
                Frame number of the input template
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
                Control terminal output: `stream` - displays to terminal immediately
                (default), `allatonce` - waits till command is finished to display
                output, `file` - writes output to file, `none` - output is ignored

Outputs::

        out_file: (a file name)
                File containing a surface-worth of per-vertex values, saved in
                'curvature' format.

.. _nipype.interfaces.freesurfer.registration.Register:


.. index:: Register

Register
--------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/freesurfer/registration.py#L301>`__

Wraps command **mris_register**

This program registers a surface to an average surface template.

Examples
~~~~~~~~
>>> from nipype.interfaces.freesurfer import Register
>>> register = Register()
>>> register.inputs.in_surf = 'lh.pial'
>>> register.inputs.in_smoothwm = 'lh.pial'
>>> register.inputs.in_sulc = 'lh.pial'
>>> register.inputs.target = 'aseg.mgz'
>>> register.inputs.out_file = 'lh.pial.reg'
>>> register.inputs.curv = True
>>> register.cmdline
'mris_register -curv lh.pial aseg.mgz lh.pial.reg'

Inputs::

        [Mandatory]
        in_sulc: (an existing file name)
                Undocumented mandatory input file
                ${SUBJECTS_DIR}/surf/{hemisphere}.sulc
        in_surf: (an existing file name)
                Surface to register, often {hemi}.sphere
                flag: %s, position: -3
        target: (an existing file name)
                The data to register to. In normal recon-all usage, this is a
                template file for average surface.
                flag: %s, position: -2

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %s
        curv: (a boolean)
                Use smoothwm curvature for final alignment
                flag: -curv
                requires: in_smoothwm
        environ: (a dictionary with keys which are a newbytes or None or a
                 newstr or None and with values which are a newbytes or None or a
                 newstr or None, nipype default value: {})
                Environment variables
        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_smoothwm: (an existing file name)
                Undocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm
        out_file: (a file name)
                Output surface file to capture registration
                flag: %s, position: -1
        subjects_dir: (an existing directory name)
                subjects directory
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
                Control terminal output: `stream` - displays to terminal immediately
                (default), `allatonce` - waits till command is finished to display
                output, `file` - writes output to file, `none` - output is ignored

Outputs::

        out_file: (a file name)
                Output surface file to capture registration

.. _nipype.interfaces.freesurfer.registration.RegisterAVItoTalairach:


.. index:: RegisterAVItoTalairach

RegisterAVItoTalairach
----------------------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/freesurfer/registration.py#L148>`__

Wraps command **avi2talxfm**

converts the vox2vox from talairach_avi to a talairach.xfm file

This is a script that converts the vox2vox from talairach_avi to a
talairach.xfm file. It is meant to replace the following cmd line:

tkregister2_cmdl         --mov $InVol         --targ $FREESURFER_HOME/average/mni305.cor.mgz         --xfmout ${XFM}         --vox2vox talsrcimg_to_${target}_t4_vox2vox.txt         --noedit         --reg talsrcimg.reg.tmp.dat
set targ = $FREESURFER_HOME/average/mni305.cor.mgz
set subject = mgh-02407836-v2
set InVol = $SUBJECTS_DIR/$subject/mri/orig.mgz
set vox2vox = $SUBJECTS_DIR/$subject/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt

Examples
~~~~~~~~

>>> from nipype.interfaces.freesurfer import RegisterAVItoTalairach
>>> register = RegisterAVItoTalairach()
>>> register.inputs.in_file = 'structural.mgz'                         # doctest: +SKIP
>>> register.inputs.target = 'mni305.cor.mgz'                          # doctest: +SKIP
>>> register.inputs.vox2vox = 'talsrcimg_to_structural_t4_vox2vox.txt' # doctest: +SKIP
>>> register.cmdline                                                   # doctest: +SKIP
'avi2talxfm structural.mgz mni305.cor.mgz talsrcimg_to_structural_t4_vox2vox.txt talairach.auto.xfm'

>>> register.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                The input file
                flag: %s, position: 0
        target: (an existing file name)
                The target file
                flag: %s, position: 1
        vox2vox: (an existing file name)
                The vox2vox file
                flag: %s, position: 2

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %s
        environ: (a dictionary with keys which are a newbytes or None or a
                 newstr or None and with values which are a newbytes or None or a
                 newstr or None, nipype default value: {})
                Environment variables
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        out_file: (a file name, nipype default value: talairach.auto.xfm)
                The transform output
                flag: %s, position: 3
        subjects_dir: (an existing directory name)
                subjects directory
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
                Control terminal output: `stream` - displays to terminal immediately
                (default), `allatonce` - waits till command is finished to display
                output, `file` - writes output to file, `none` - output is ignored

Outputs::

        log_file: (an existing file name, nipype default value:
                 output.nipype)
                The output log
        out_file: (a file name)
                The output file for RegisterAVItoTalairach
