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# interfaces.freesurfer.utils

## ApplyMask

Link to code

Wraps command mri_mask

Use Freesurfer’s mri_mask to apply a mask to an image.

The mask file need not be binarized; it can be thresholded above a given value before application. It can also optionally be transformed into input space with an LTA matrix.

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input image (will be masked)
            flag: %s, position: -3
    mask_file: (an existing file name)
            image defining mask space
            flag: %s, position: -2
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', 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
    invert_xfm: (a boolean)
            invert transformation
            flag: -invert
    mask_thresh: (a float)
            threshold mask before applying
            flag: -T %.4f
    out_file: (a file name)
            final image to write
            flag: %s, position: -1
    subjects_dir: (an existing directory name)
            subjects directory
    use_abs: (a boolean)
            take absolute value of mask before applying
            flag: -abs
    xfm_file: (an existing file name)
            LTA-format transformation matrix to align mask with input
            flag: -xform %s
    xfm_source: (an existing file name)
            image defining transform source space
            flag: -lta_src %s
    xfm_target: (an existing file name)
            image defining transform target space
            flag: -lta_dst %s

Outputs:

    out_file: (an existing file name)
            masked image

## ExtractMainComponent

Link to code

Wraps command mris_extract_main_component

Extract the main component of a tesselated surface

### Examples

    >>> from nipype.interfaces.freesurfer import ExtractMainComponent
    >>> mcmp = ExtractMainComponent(in_file='lh.pial')
    >>> mcmp.cmdline
    'mris_extract_main_component lh.pial lh.maincmp'

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            input surface file
            flag: %s, position: 1
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', 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)
            surface containing main component
            flag: %s, position: 2

Outputs:

    out_file: (an existing file name)
            surface containing main component

## MRIMarchingCubes

Link to code

Wraps command mri_mc

Uses Freesurfer’s mri_mc to create surfaces by tessellating a given input volume

### Example

    >>> import nipype.interfaces.freesurfer as fs
    >>> mc = fs.MRIMarchingCubes()
    >>> mc.inputs.in_file = 'aseg.mgz'
    >>> mc.inputs.label_value = 17
    >>> mc.inputs.out_file = 'lh.hippocampus'
    >>> mc.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            Input volume to tesselate voxels from.
            flag: %s, position: 1
    label_value: (an integer)
            Label value which to tesselate from the input volume. (integer, if
            input is "filled.mgz" volume, 127 is rh, 255 is lh)
            flag: %d, position: 2
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    connectivity_value: (an integer, nipype default value: 1)
            Alter the marching cubes connectivity: 1=6+,2=18,3=6,4=26
            (default=1)
            flag: %d, position: -1
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', 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)
            output filename or True to generate one
            flag: ./%s, position: -2
    subjects_dir: (an existing directory name)
            subjects directory

Outputs:

    surface: (an existing file name)
            binary surface of the tessellation

## MRIPretess

Link to code

Wraps command mri_pretess

Uses Freesurfer’s mri_pretess to prepare volumes to be tessellated.

### Description

Changes white matter (WM) segmentation so that the neighbors of all voxels labeled as WM have a face in common - no edges or corners allowed.

### Example

    >>> import nipype.interfaces.freesurfer as fs
    >>> pretess = fs.MRIPretess()
    >>> pretess.inputs.in_filled = 'wm.mgz'
    >>> pretess.inputs.in_norm = 'norm.mgz'
    >>> pretess.inputs.nocorners = True
    >>> pretess.cmdline
    'mri_pretess -nocorners wm.mgz wm norm.mgz wm_pretesswm.mgz'
    >>> pretess.run()

Inputs:

    [Mandatory]
    in_filled: (an existing file name)
            filled volume, usually wm.mgz
            flag: %s, position: -4
    in_norm: (an existing file name)
            the normalized, brain-extracted T1w image. Usually norm.mgz
            flag: %s, position: -2
    label: (a string or an integer, nipype default value: wm)
            label to be picked up, can be a Freesurfer's string like 'wm' or a
            label value (e.g. 127 for rh or 255 for lh)
            flag: %s, position: -3
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', 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
    keep: (a boolean)
            keep WM edits
            flag: -keep
    nocorners: (a boolean)
            do not remove corner configurations in addition to edge ones.
            flag: -nocorners
    out_file: (a file name)
            the output file after mri_pretess.
            flag: %s, position: -1
    subjects_dir: (an existing directory name)
            subjects directory
    test: (a boolean)
            adds a voxel that should be removed by mri_pretess. The value of the
            voxel is set to that of an ON-edited WM, so it should be kept with
            -keep. The output will NOT be saved.
            flag: -test

Outputs:

    out_file: (an existing file name)
            output file after mri_pretess

## MRITessellate

Link to code

Wraps command mri_tessellate

Uses Freesurfer’s mri_tessellate to create surfaces by tessellating a given input volume

### Example

    >>> import nipype.interfaces.freesurfer as fs
    >>> tess = fs.MRITessellate()
    >>> tess.inputs.in_file = 'aseg.mgz'
    >>> tess.inputs.label_value = 17
    >>> tess.inputs.out_file = 'lh.hippocampus'
    >>> tess.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            Input volume to tesselate voxels from.
            flag: %s, position: -3
    label_value: (an integer)
            Label value which to tesselate from the input volume. (integer, if
            input is "filled.mgz" volume, 127 is rh, 255 is lh)
            flag: %d, position: -2
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', 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)
            output filename or True to generate one
            flag: ./%s, position: -1
    subjects_dir: (an existing directory name)
            subjects directory
    tesselate_all_voxels: (a boolean)
            Tessellate the surface of all voxels with different labels
            flag: -a
    use_real_RAS_coordinates: (a boolean)
            Saves surface with real RAS coordinates where c_(r,a,s) != 0
            flag: -n

Outputs:

    surface: (an existing file name)
            binary surface of the tessellation

## MRIsConvert

Link to code

Wraps command mris_convert

Uses Freesurfer’s mris_convert to convert surface files to various formats

### Example

    >>> import nipype.interfaces.freesurfer as fs
    >>> mris = fs.MRIsConvert()
    >>> mris.inputs.in_file = 'lh.pial'
    >>> mris.inputs.out_datatype = 'gii'
    >>> mris.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            File to read/convert
            flag: %s, position: -2
    out_datatype: ('ico' or 'tri' or 'stl' or 'vtk' or 'gii' or 'mgh' or
             'mgz')
            These file formats are supported: ASCII: .ascICO: .ico, .tri GEO:
            .geo STL: .stl VTK: .vtk GIFTI: .gii MGH surface-encoded 'volume':
            .mgh, .mgz
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    annot_file: (an existing file name)
            input is annotation or gifti label data
            flag: --annot %s
    args: (a string)
            Additional parameters to the command
            flag: %s
    dataarray_num: (an integer)
            if input is gifti, 'num' specifies which data array to use
            flag: --da_num %d
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    functional_file: (an existing file name)
            input is functional time-series or other multi-frame data (must
            specify surface)
            flag: -f %s
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    label_file: (an existing file name)
            infile is .label file, label is name of this label
            flag: --label %s
    labelstats_outfile: (a file name)
            outfile is name of gifti file to which label stats will be written
            flag: --labelstats %s
    normal: (a boolean)
            output is an ascii file where vertex data
            flag: -n
    origname: (a string)
            read orig positions
            flag: -o %s
    out_file: (a file name)
            output filename or True to generate one
            flag: ./%s, position: -1
    parcstats_file: (an existing file name)
            infile is name of text file containing label/val pairs
            flag: --parcstats %s
    patch: (a boolean)
            input is a patch, not a full surface
            flag: -p
    rescale: (a boolean)
            rescale vertex xyz so total area is same as group average
            flag: -r
    scalarcurv_file: (an existing file name)
            input is scalar curv overlay file (must still specify surface)
            flag: -c %s
    scale: (a float)
            scale vertex xyz by scale
            flag: -s %.3f
    subjects_dir: (an existing directory name)
            subjects directory
    talairachxfm_subjid: (a string)
            apply talairach xfm of subject to vertex xyz
            flag: -t %s
    vertex: (a boolean)
            Writes out neighbors of a vertex in each row
            flag: -v
    xyz_ascii: (a boolean)
            Print only surface xyz to ascii file
            flag: -a

Outputs:

    converted: (an existing file name)
            converted output surface

## MakeAverageSubject

Link to code

Wraps command make_average_subject

Make an average freesurfer subject

### Examples

    >>> from nipype.interfaces.freesurfer import MakeAverageSubject
    >>> avg = MakeAverageSubject(subjects_ids=['s1', 's2'])
    >>> avg.cmdline
    'make_average_subject --out average --subjects s1 s2'

Inputs:

    [Mandatory]
    subjects_ids: (a list of items which are a string)
            freesurfer subjects ids to average
            flag: --subjects %s
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', 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_name: (a file name, nipype default value: average)
            name for the average subject
            flag: --out %s
    subjects_dir: (an existing directory name)
            subjects directory

Outputs:

    average_subject_name: (a string)
            Output registration file

## SampleToSurface

Link to code

Wraps command mri_vol2surf

Sample a volume to the cortical surface using Freesurfer’s mri_vol2surf.

You must supply a sampling method, range, and units. You can project either a given distance (in mm) or a given fraction of the cortical thickness at that vertex along the surface normal from the target surface, and then set the value of that vertex to be either the value at that point or the average or maximum value found along the projection vector.

By default, the surface will be saved as a vector with a length equal to the number of vertices on the target surface. This is not a problem for Freesurfer programs, but if you intend to use the file with interfaces to another package, you must set the `reshape` input to True, which will factor the surface vector into a matrix with dimensions compatible with proper Nifti files.

### Examples

    >>> import nipype.interfaces.freesurfer as fs
    >>> sampler = fs.SampleToSurface(hemi="lh")
    >>> sampler.inputs.source_file = "cope1.nii.gz"
    >>> sampler.inputs.reg_file = "register.dat"
    >>> sampler.inputs.sampling_method = "average"
    >>> sampler.inputs.sampling_range = 1
    >>> sampler.inputs.sampling_units = "frac"
    >>> res = sampler.run()

Inputs:

    [Mandatory]
    hemi: ('lh' or 'rh')
            target hemisphere
            flag: --hemi %s
    mni152reg: (a boolean)
            source volume is in MNI152 space
            flag: --mni152reg
            mutually_exclusive: reg_file, reg_header, mni152reg
    projection_stem: (a string)
            stem for precomputed linear estimates and volume fractions
            mutually_exclusive: sampling_method
    reg_file: (an existing file name)
            source-to-reference registration file
            flag: --reg %s
            mutually_exclusive: reg_file, reg_header, mni152reg
    reg_header: (a boolean)
            register based on header geometry
            flag: --regheader %s
            mutually_exclusive: reg_file, reg_header, mni152reg
            requires: subject_id
    sampling_method: ('point' or 'max' or 'average')
            how to sample -- at a point or at the max or average over a range
            flag: %s
            mutually_exclusive: projection_stem
            requires: sampling_range, sampling_units
    source_file: (an existing file name)
            volume to sample values from
            flag: --mov %s
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    apply_rot: (a tuple of the form: (a float, a float, a float))
            rotation angles (in degrees) to apply to reg matrix
            flag: --rot %.3f %.3f %.3f
    apply_trans: (a tuple of the form: (a float, a float, a float))
            translation (in mm) to apply to reg matrix
            flag: --trans %.3f %.3f %.3f
    args: (a string)
            Additional parameters to the command
            flag: %s
    cortex_mask: (a boolean)
            mask the target surface with hemi.cortex.label
            flag: --cortex
            mutually_exclusive: mask_label
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    fix_tk_reg: (a boolean)
            make reg matrix round-compatible
            flag: --fixtkreg
    float2int_method: ('round' or 'tkregister')
            method to convert reg matrix values (default is round)
            flag: --float2int %s
    frame: (an integer)
            save only one frame (0-based)
            flag: --frame %d
    hits_file: (a boolean or an existing file name)
            save image with number of hits at each voxel
            flag: --srchit %s
    hits_type: ('cor' or 'mgh' or 'mgz' or 'minc' or 'analyze' or
             'analyze4d' or 'spm' or 'afni' or 'brik' or 'bshort' or 'bfloat' or
             'sdt' or 'outline' or 'otl' or 'gdf' or 'nifti1' or 'nii' or
             'niigz')
            hits file type
            flag: --srchit_type
    ico_order: (an integer)
            icosahedron order when target_subject is 'ico'
            flag: --icoorder %d
            requires: target_subject
    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_method: ('nearest' or 'trilinear')
            interpolation method
            flag: --interp %s
    mask_label: (an existing file name)
            label file to mask output with
            flag: --mask %s
            mutually_exclusive: cortex_mask
    no_reshape: (a boolean)
            do not reshape surface vector (default)
            flag: --noreshape
            mutually_exclusive: reshape
    out_file: (a file name)
            surface file to write
            flag: --o %s
    out_type: ('cor' or 'mgh' or 'mgz' or 'minc' or 'analyze' or
             'analyze4d' or 'spm' or 'afni' or 'brik' or 'bshort' or 'bfloat' or
             'sdt' or 'outline' or 'otl' or 'gdf' or 'nifti1' or 'nii' or
             'niigz')
            output file type
            flag: --out_type %s
    override_reg_subj: (a boolean)
            override the subject in the reg file header
            flag: --srcsubject %s
            requires: subject_id
    reference_file: (an existing file name)
            reference volume (default is orig.mgz)
            flag: --ref %s
    reshape: (a boolean)
            reshape surface vector to fit in non-mgh format
            flag: --reshape
            mutually_exclusive: no_reshape
    reshape_slices: (an integer)
            number of 'slices' for reshaping
            flag: --rf %d
    sampling_range: (a float or a tuple of the form: (a float, a float, a
             float))
            sampling range - a point or a tuple of (min, max, step)
    sampling_units: ('mm' or 'frac')
            sampling range type -- either 'mm' or 'frac'
    scale_input: (a float)
            multiple all intensities by scale factor
            flag: --scale %.3f
    smooth_surf: (a float)
            smooth output surface (mm fwhm)
            flag: --surf-fwhm %.3f
    smooth_vol: (a float)
            smooth input volume (mm fwhm)
            flag: --fwhm %.3f
    subject_id: (a string)
            subject id
    subjects_dir: (an existing directory name)
            subjects directory
    surf_reg: (a boolean)
            use surface registration to target subject
            flag: --surfreg
            requires: target_subject
    surface: (a string)
            target surface (default is white)
            flag: --surf %s
    target_subject: (a string)
            sample to surface of different subject than source
            flag: --trgsubject %s
    vox_file: (a boolean or a file name)
            text file with the number of voxels intersecting the surface
            flag: --nvox %s

Outputs:

    hits_file: (an existing file name)
            image with number of hits at each voxel
    out_file: (an existing file name)
            surface file
    vox_file: (an existing file name)
            text file with the number of voxels intersecting the surface

## SmoothTessellation

Link to code

Wraps command mris_smooth

This program smooths the tessellation of a surface using ‘mris_smooth’

See also

SurfaceSmooth() Interface
  For smoothing a scalar field along a surface manifold

### Example

    >>> import nipype.interfaces.freesurfer as fs
    >>> smooth = fs.SmoothTessellation()
    >>> smooth.inputs.in_file = 'lh.hippocampus.stl'
    >>> smooth.run()

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            Input volume to tesselate voxels from.
            flag: %s, position: 1
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    curvature_averaging_iterations: (an integer, nipype default value:
             10)
            Number of curvature averaging iterations (default=10)
            flag: -a %d, position: -1
    disable_estimates: (a boolean)
            Disables the writing of curvature and area estimates
            flag: -nw
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    gaussian_curvature_norm_steps: (an integer)
            Use Gaussian curvature smoothing
            flag: %d , position: 4
    gaussian_curvature_smoothing_steps: (an integer)
            Use Gaussian curvature smoothing
            flag: %d, position: 5
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    normalize_area: (a boolean)
            Normalizes the area after smoothing
            flag: -area
    out_area_file: (a file name)
            Write area to ?h.areaname (default "area")
            flag: -b %s
    out_curvature_file: (a file name)
            Write curvature to ?h.curvname (default "curv")
            flag: -c %s
    out_file: (a file name)
            output filename or True to generate one
            flag: %s, position: 2
    smoothing_iterations: (an integer, nipype default value: 10)
            Number of smoothing iterations (default=10)
            flag: -n %d, position: -2
    snapshot_writing_iterations: (an integer)
            Write snapshot every "n" iterations
            flag: -w %d
    subjects_dir: (an existing directory name)
            subjects directory
    use_gaussian_curvature_smoothing: (a boolean)
            Use Gaussian curvature smoothing
            flag: -g, position: 3
    use_momentum: (a boolean)
            Uses momentum
            flag: -m

Outputs:

    surface: (an existing file name)
            Smoothed surface file

## Surface2VolTransform

Link to code

Wraps command mri_surf2vol

Use FreeSurfer mri_surf2vol to apply a transform.

### Examples

    >>> from nipype.interfaces.freesurfer import Surface2VolTransform
    >>> xfm2vol = Surface2VolTransform()
    >>> xfm2vol.inputs.source_file = 'lh.cope1.mgz'
    >>> xfm2vol.inputs.reg_file = 'register.mat'
    >>> xfm2vol.inputs.hemi = 'lh'
    >>> xfm2vol.inputs.template_file = 'cope1.nii.gz'
    >>> xfm2vol.inputs.subjects_dir = '.'
    >>> xfm2vol.cmdline
    'mri_surf2vol --hemi lh --volreg register.mat --surfval lh.cope1.mgz --sd . --template cope1.nii.gz --outvol lh.cope1_asVol.nii --vtxvol lh.cope1_asVol_vertex.nii'
    >>> res = xfm2vol.run()

Inputs:

    [Mandatory]
    hemi: (a string)
            hemisphere of data
            flag: --hemi %s
    reg_file: (an existing file name)
            tkRAS-to-tkRAS matrix (tkregister2 format)
            flag: --volreg %s
            mutually_exclusive: subject_id
    source_file: (an existing file name)
            This is the source of the surface values
            flag: --surfval %s
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', 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
    mkmask: (a boolean)
            make a mask instead of loading surface values
            flag: --mkmask
    projfrac: (a float)
            thickness fraction
            flag: --projfrac %s
    subject_id: (a string)
            subject id
            flag: --identity %s
            mutually_exclusive: reg_file
    subjects_dir: (a string)
            freesurfer subjects directory defaults to $SUBJECTS_DIR
            flag: --sd %s
    surf_name: (a string)
            surfname (default is white)
            flag: --surf %s
    template_file: (an existing file name)
            Output template volume
            flag: --template %s
    transformed_file: (a file name)
            Output volume
            flag: --outvol %s
    vertexvol_file: (a file name)
            Path name of the vertex output volume, which is the same as output
            volume except that the value of each voxel is the vertex-id that is
            mapped to that voxel.
            flag: --vtxvol %s

Outputs:

    transformed_file: (an existing file name)
            Path to output file if used normally
    vertexvol_file: (a file name)
            vertex map volume path id. Optional

## SurfaceSmooth

Link to code

Wraps command mri_surf2surf

Smooth a surface image with mri_surf2surf.

The surface is smoothed by an interative process of averaging the value at each vertex with those of its adjacent neighbors. You may supply either the number of iterations to run or a desired effective FWHM of the smoothing process. If the latter, the underlying program will calculate the correct number of iterations internally.

See also

SmoothTessellation() Interface
  For smoothing a tessellated surface (e.g. in gifti or .stl)

### Examples

    >>> import nipype.interfaces.freesurfer as fs
    >>> smoother = fs.SurfaceSmooth()
    >>> smoother.inputs.in_file = "lh.cope1.mgz"
    >>> smoother.inputs.subject_id = "subj_1"
    >>> smoother.inputs.hemi = "lh"
    >>> smoother.inputs.fwhm = 5
    >>> smoother.run()

Inputs:

    [Mandatory]
    hemi: ('lh' or 'rh')
            hemisphere to operate on
            flag: --hemi %s
    in_file: (a file name)
            source surface file
            flag: --sval %s
    subject_id: (a string)
            subject id of surface file
            flag: --s %s
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    cortex: (a boolean, nipype default value: True)
            only smooth within $hemi.cortex.label
            flag: --cortex
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    fwhm: (a float)
            effective FWHM of the smoothing process
            flag: --fwhm %.4f
            mutually_exclusive: smooth_iters
    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)
            surface file to write
            flag: --tval %s
    reshape: (a boolean)
            reshape surface vector to fit in non-mgh format
            flag: --reshape
    smooth_iters: (an integer)
            iterations of the smoothing process
            flag: --smooth %d
            mutually_exclusive: fwhm
    subjects_dir: (an existing directory name)
            subjects directory

Outputs:

    out_file: (an existing file name)
            smoothed surface file

## SurfaceSnapshots

Link to code

Wraps command tksurfer

Use Tksurfer to save pictures of the cortical surface.

By default, this takes snapshots of the lateral, medial, ventral, and dorsal surfaces. See the `six_images` option to add the anterior and posterior surfaces.

You may also supply your own tcl script (see the Freesurfer wiki for information on scripting tksurfer). The screenshot stem is set as the environment variable “_SNAPSHOT_STEM”, which you can use in your own scripts.

Node that this interface will not run if you do not have graphics enabled on your system.

### Examples

    >>> import nipype.interfaces.freesurfer as fs
    >>> shots = fs.SurfaceSnapshots(subject_id="fsaverage", hemi="lh", surface="pial")
    >>> shots.inputs.overlay = "zstat1.nii.gz"
    >>> shots.inputs.overlay_range = (2.3, 6)
    >>> shots.inputs.overlay_reg = "register.dat"
    >>> res = shots.run()

Inputs:

    [Mandatory]
    hemi: ('lh' or 'rh')
            hemisphere to visualize
            flag: %s, position: 2
    subject_id: (a string)
            subject to visualize
            flag: %s, position: 1
    surface: (a string)
            surface to visualize
            flag: %s, position: 3
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    annot_file: (an existing file name)
            path to annotation file to display
            flag: -annotation %s
            mutually_exclusive: annot_name
    annot_name: (a string)
            name of annotation to display (must be in $subject/label directory
            flag: -annotation %s
            mutually_exclusive: annot_file
    args: (a string)
            Additional parameters to the command
            flag: %s
    colortable: (an existing file name)
            load colortable file
            flag: -colortable %s
    demean_overlay: (a boolean)
            remove mean from overlay
            flag: -zm
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    identity_reg: (a boolean)
            use the identity matrix to register the overlay to the surface
            flag: -overlay-reg-identity
            mutually_exclusive: overlay_reg, identity_reg, mni152_reg
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    invert_overlay: (a boolean)
            invert the overlay display
            flag: -invphaseflag 1
    label_file: (an existing file name)
            path to label file to display
            flag: -label %s
            mutually_exclusive: label_name
    label_name: (a string)
            name of label to display (must be in $subject/label directory
            flag: -label %s
            mutually_exclusive: label_file
    label_outline: (a boolean)
            draw label/annotation as outline
            flag: -label-outline
    label_under: (a boolean)
            draw label/annotation under overlay
            flag: -labels-under
    mni152_reg: (a boolean)
            use to display a volume in MNI152 space on the average subject
            flag: -mni152reg
            mutually_exclusive: overlay_reg, identity_reg, mni152_reg
    orig_suffix: (a string)
            set the orig surface suffix string
            flag: -orig %s
    overlay: (an existing file name)
            load an overlay volume/surface
            flag: -overlay %s
            requires: overlay_range
    overlay_range: (a float or a tuple of the form: (a float, a float) or
             a tuple of the form: (a float, a float, a float))
            overlay range--either min, (min, max) or (min, mid, max)
            flag: %s
    overlay_range_offset: (a float)
            overlay range will be symettric around offset value
            flag: -foffset %.3f
    overlay_reg: (a file name)
            registration matrix file to register overlay to surface
            flag: -overlay-reg %s
            mutually_exclusive: overlay_reg, identity_reg, mni152_reg
    patch_file: (an existing file name)
            load a patch
            flag: -patch %s
    reverse_overlay: (a boolean)
            reverse the overlay display
            flag: -revphaseflag 1
    screenshot_stem: (a string)
            stem to use for screenshot file names
    show_color_scale: (a boolean)
            display the color scale bar
            flag: -colscalebarflag 1
    show_color_text: (a boolean)
            display text in the color scale bar
            flag: -colscaletext 1
    show_curv: (a boolean)
            show curvature
            flag: -curv
            mutually_exclusive: show_gray_curv
    show_gray_curv: (a boolean)
            show curvature in gray
            flag: -gray
            mutually_exclusive: show_curv
    six_images: (a boolean)
            also take anterior and posterior snapshots
    sphere_suffix: (a string)
            set the sphere.reg suffix string
            flag: -sphere %s
    stem_template_args: (a list of items which are a string)
            input names to use as arguments for a string-formated stem template
            requires: screenshot_stem
    subjects_dir: (an existing directory name)
            subjects directory
    tcl_script: (an existing file name)
            override default screenshot script
            flag: %s
    truncate_overlay: (a boolean)
            truncate the overlay display
            flag: -truncphaseflag 1

Outputs:

    snapshots: (an existing file name)
            tiff images of the surface from different perspectives

## SurfaceTransform

Link to code

Wraps command mri_surf2surf

Transform a surface file from one subject to another via a spherical registration.

Both the source and target subject must reside in your Subjects Directory, and they must have been processed with recon-all, unless you are transforming to one of the icosahedron meshes.

### Examples

    >>> from nipype.interfaces.freesurfer import SurfaceTransform
    >>> sxfm = SurfaceTransform()
    >>> sxfm.inputs.source_file = "lh.cope1.nii.gz"
    >>> sxfm.inputs.source_subject = "my_subject"
    >>> sxfm.inputs.target_subject = "fsaverage"
    >>> sxfm.inputs.hemi = "lh"
    >>> sxfm.run()

Inputs:

    [Mandatory]
    hemi: ('lh' or 'rh')
            hemisphere to transform
            flag: --hemi %s
    source_annot_file: (an existing file name)
            surface annotation file
            flag: --sval-annot %s
            mutually_exclusive: source_file
    source_file: (an existing file name)
            surface file with source values
            flag: --sval %s
            mutually_exclusive: source_annot_file
    source_subject: (a string)
            subject id for source surface
            flag: --srcsubject %s
    target_subject: (a string)
            subject id of target surface
            flag: --trgsubject %s
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', 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)
            surface file to write
            flag: --tval %s
    reshape: (a boolean)
            reshape output surface to conform with Nifti
            flag: --reshape
    reshape_factor: (an integer)
            number of slices in reshaped image
            flag: --reshape-factor
    source_type: ('cor' or 'mgh' or 'mgz' or 'minc' or 'analyze' or
             'analyze4d' or 'spm' or 'afni' or 'brik' or 'bshort' or 'bfloat' or
             'sdt' or 'outline' or 'otl' or 'gdf' or 'nifti1' or 'nii' or
             'niigz')
            source file format
            flag: --sfmt %s
            requires: source_file
    subjects_dir: (an existing directory name)
            subjects directory
    target_ico_order: (1 or 2 or 3 or 4 or 5 or 6 or 7)
            order of the icosahedron if target_subject is 'ico'
            flag: --trgicoorder %d
    target_type: ('cor' or 'mgh' or 'mgz' or 'minc' or 'analyze' or
             'analyze4d' or 'spm' or 'afni' or 'brik' or 'bshort' or 'bfloat' or
             'sdt' or 'outline' or 'otl' or 'gdf' or 'nifti1' or 'nii' or
             'niigz')
            output format
            flag: --tfmt %s

Outputs:

    out_file: (an existing file name)
            transformed surface file

## Tkregister2

Link to code

Wraps command tkregister2

### Examples

Get transform matrix between orig (tkRAS) and native (scannerRAS) coordinates in Freesurfer. Implements the first step of mapping surfaces to native space in this guide.

    >>> from nipype.interfaces.freesurfer import Tkregister2
    >>> tk2 = Tkregister2(reg_file='T1_to_native.dat')
    >>> tk2.inputs.moving_image = 'T1.mgz'
    >>> tk2.inputs.target_image = 'structural.nii'
    >>> tk2.inputs.reg_header = True
    >>> tk2.cmdline
    'tkregister2 --mov T1.mgz --noedit --reg T1_to_native.dat --regheader --targ structural.nii'
    >>> tk2.run()

The example below uses tkregister2 without the manual editing stage to convert FSL-style registration matrix (.mat) to FreeSurfer-style registration matrix (.dat)

    >>> from nipype.interfaces.freesurfer import Tkregister2
    >>> tk2 = Tkregister2()
    >>> tk2.inputs.moving_image = 'epi.nii'
    >>> tk2.inputs.fsl_in_matrix = 'flirt.mat'
    >>> tk2.cmdline
    'tkregister2 --fsl flirt.mat --mov epi.nii --noedit --reg register.dat'
    >>> tk2.run()

Inputs:

    [Mandatory]
    moving_image: (an existing file name)
            moving volume
            flag: --mov %s
    reg_file: (a file name, nipype default value: register.dat)
            freesurfer-style registration file
            flag: --reg %s
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    fsl_in_matrix: (an existing file name)
            fsl-style registration input matrix
            flag: --fsl %s
    fsl_out: (a file name)
            compute an FSL-compatible resgitration matrix
            flag: --fslregout %s
    fstal: (a boolean)
            set mov to be tal and reg to be tal xfm
            flag: --fstal
            mutually_exclusive: target_image, moving_image
    fstarg: (a boolean)
            use subject's T1 as reference
            flag: --fstarg
            mutually_exclusive: target_image
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    movscale: (a float)
            adjust registration matrix to scale mov
            flag: --movscale %f
    noedit: (a boolean, nipype default value: True)
            do not open edit window (exit)
            flag: --noedit
    reg_header: (a boolean)
            compute regstration from headers
            flag: --regheader
    subject_id: (a string)
            freesurfer subject ID
            flag: --s %s
    subjects_dir: (an existing directory name)
            subjects directory
    target_image: (an existing file name)
            target volume
            flag: --targ %s
            mutually_exclusive: fstarg
    xfm: (an existing file name)
            use a matrix in MNI coordinates as initial registration
            flag: --xfm %s

Outputs:

    fsl_file: (a file name)
            FSL-style registration file
    reg_file: (an existing file name)
            freesurfer-style registration file