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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)
    mask_file: (an existing file name)
            image defining mask space
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    args: (a string)
            Additional parameters to the command
    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
    mask_thresh: (a float)
            threshold mask before applying
    out_file: (a file name)
            final image to write
    subjects_dir: (an existing directory name)
            subjects directory
    use_abs: (a boolean)
            take absolute value of mask before applying
    xfm_file: (an existing file name)
            LTA-format transformation matrix to align mask with input
    xfm_source: (an existing file name)
            image defining transform source space
    xfm_target: (an existing file name)
            image defining transform target space

Outputs:

    out_file: (an existing file name)
            masked image

## 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.
    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)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    args: (a string)
            Additional parameters to the command
    connectivity_value: (an integer, nipype default value: 1)
            Alter the marching cubes connectivity: 1=6+,2=18,3=6,4=26 (default=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
    subjects_dir: (an existing directory name)
            subjects directory

Outputs:

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

## 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.
    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)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    args: (a string)
            Additional parameters to the command
    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
    subjects_dir: (an existing directory name)
            subjects directory
    tesselate_all_voxels: (a boolean)
            Tessellate the surface of all voxels with different labels
    use_real_RAS_coordinates: (a boolean)
            Saves surface with real RAS coordinates where c_(r,a,s) != 0

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
    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

    [Optional]
    annot_file: (an existing file name)
            input is annotation or gifti label data
    args: (a string)
            Additional parameters to the command
    dataarray_num: (an integer)
            if input is gifti, 'num' specifies which data array to use
    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)
    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
    labelstats_outfile: (a file name)
            outfile is name of gifti file to which label stats will be written
    normal: (a boolean)
            output is an ascii file where vertex data
    origname: (a string)
            read orig positions
    out_file: (a file name)
            output filename or True to generate one
    parcstats_file: (an existing file name)
            infile is name of text file containing label/val pairs
    patch: (a boolean)
            input is a patch, not a full surface
    rescale: (a boolean)
            rescale vertex xyz so total area is same as group average
    scalarcurv_file: (an existing file name)
            input is scalar curv overlay file (must still specify surface)
    scale: (a float)
            scale vertex xyz by scale
    subjects_dir: (an existing directory name)
            subjects directory
    talairachxfm_subjid: (a string)
            apply talairach xfm of subject to vertex xyz
    vertex: (a boolean)
            Writes out neighbors of a vertex in each row
    xyz_ascii: (a boolean)
            Print only surface xyz to ascii file

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
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    args: (a string)
            Additional parameters to the command
    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
    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
    projection_stem: (a string)
            stem for precomputed linear estimates and volume fractions
            mutually_exclusive: sampling_method
    sampling_method: ('point' or 'max' or 'average')
            how to sample -- at a point or at the max or average over a range
            mutually_exclusive: projection_stem
            requires: sampling_range, sampling_units
    source_file: (an existing file name)
            volume to sample values from
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    apply_rot: (a tuple of the form: (a float, a float, a float))
            rotation angles (in degrees) to apply to reg matrix
    apply_trans: (a tuple of the form: (a float, a float, a float))
            translation (in mm) to apply to reg matrix
    args: (a string)
            Additional parameters to the command
    cortex_mask: (a boolean)
            mask the target surface with hemi.cortex.label
            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
    float2int_method: ('round' or 'tkregister')
            method to convert reg matrix values (default is round)
    frame: (an integer)
            save only one frame (0-based)
    hits_file: (a boolean or an existing file name)
            save image with number of hits at each voxel
    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
    ico_order: (an integer)
            icosahedron order when target_subject is 'ico'
            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
    mask_label: (an existing file name)
            label file to mask output with
            mutually_exclusive: cortex_mask
    mni152reg: (a boolean)
            source volume is in MNI152 space
            mutually_exclusive: reg_file, reg_header, mni152reg
    no_reshape: (a boolean)
            do not reshape surface vector (default)
            mutually_exclusive: reshape
    out_file: (a file name)
            surface file to write
    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
    override_reg_subj: (a boolean)
            override the subject in the reg file header
            requires: subject_id
    reference_file: (an existing file name)
            reference volume (default is orig.mgz)
    reg_file: (an existing file name)
            source-to-reference registration file
            mutually_exclusive: reg_file, reg_header, mni152reg
    reg_header: (a boolean)
            register based on header geometry
            mutually_exclusive: reg_file, reg_header, mni152reg
            requires: subject_id
    reshape: (a boolean)
            reshape surface vector to fit in non-mgh format
            mutually_exclusive: no_reshape
    reshape_slices: (an integer)
            number of 'slices' for reshaping
    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
    smooth_surf: (a float)
            smooth output surface (mm fwhm)
    smooth_vol: (a float)
            smooth input volume (mm fwhm)
    subject_id: (a string)
            subject id
    subjects_dir: (an existing directory name)
            subjects directory
    surf_reg: (a boolean)
            use surface registration to target subject
            requires: target_subject
    surface: (a string)
            target surface (default is white)
    target_subject: (a string)
            sample to surface of different subject than source
    vox_file: (a boolean or a file name)
            text file with the number of voxels intersecting the surface

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.
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    args: (a string)
            Additional parameters to the command
    curvature_averaging_iterations: (an integer, nipype default value: 10)
            Number of curvature averaging iterations (default=10)
    disable_estimates: (a boolean)
            Disables the writing of curvature and area estimates
    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
    gaussian_curvature_smoothing_steps: (an integer)
            Use Gaussian curvature smoothing
    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
    out_area_file: (a file name)
            Write area to ?h.areaname (default "area")
    out_curvature_file: (a file name)
            Write curvature to ?h.curvname (default "curv")
    out_file: (a file name)
            output filename or True to generate one
    smoothing_iterations: (an integer, nipype default value: 10)
            Number of smoothing iterations (default=10)
    snapshot_writing_iterations: (an integer)
            Write snapshot every "n" iterations
    subjects_dir: (an existing directory name)
            subjects directory
    use_gaussian_curvature_smoothing: (a boolean)
            Use Gaussian curvature smoothing
    use_momentum: (a boolean)
            Uses momentum

Outputs:

    surface: (an existing file name)
            Smoothed surface file

## 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
    in_file: (a file name)
            source surface file
    subject_id: (a string)
            subject id of surface file
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    args: (a string)
            Additional parameters to the command
    cortex: (a boolean, nipype default value: True)
            only smooth within $hemi.cortex.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
    fwhm: (a float)
            effective FWHM of the smoothing process
            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
    reshape: (a boolean)
            reshape surface vector to fit in non-mgh format
    smooth_iters: (an integer)
            iterations of the smoothing process
            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
    subject_id: (a string)
            subject to visualize
    surface: (a string)
            surface to visualize
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    annot_file: (an existing file name)
            path to annotation file to display
            mutually_exclusive: annot_name
    annot_name: (a string)
            name of annotation to display (must be in $subject/label directory
            mutually_exclusive: annot_file
    args: (a string)
            Additional parameters to the command
    colortable: (an existing file name)
            load colortable file
    demean_overlay: (a boolean)
            remove mean from overlay
    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
            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
    label_file: (an existing file name)
            path to label file to display
            mutually_exclusive: label_name
    label_name: (a string)
            name of label to display (must be in $subject/label directory
            mutually_exclusive: label_file
    label_outline: (a boolean)
            draw label/annotation as outline
    label_under: (a boolean)
            draw label/annotation under overlay
    mni152_reg: (a boolean)
            use to display a volume in MNI152 space on the average subject
            mutually_exclusive: overlay_reg, identity_reg, mni152_reg
    orig_suffix: (a string)
            set the orig surface suffix string
    overlay: (an existing file name)
            load an overlay volume/surface
            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)
    overlay_range_offset: (a float)
            overlay range will be symettric around offset value
    overlay_reg: (a file name)
            registration matrix file to register overlay to surface
            mutually_exclusive: overlay_reg, identity_reg, mni152_reg
    patch_file: (an existing file name)
            load a patch
    reverse_overlay: (a boolean)
            reverse the overlay display
    screenshot_stem: (a string)
            stem to use for screenshot file names
    show_color_scale: (a boolean)
            display the color scale bar
    show_color_text: (a boolean)
            display text in the color scale bar
    show_curv: (a boolean)
            show curvature
            mutually_exclusive: show_gray_curv
    show_gray_curv: (a boolean)
            show curvature in 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
    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
    truncate_overlay: (a boolean)
            truncate the overlay display

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
    source_annot_file: (an existing file name)
            mutually_exclusive: source_file
    source_file: (an existing file name)
            mutually_exclusive: source_annot_file
    source_subject: (a string)
    target_subject: (a string)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    args: (a string)
            Additional parameters to the command
    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
    reshape: (a boolean)
    reshape_factor: (an integer)
    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')
            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)
    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')

Outputs:

    out_file: (an existing file name)
            transformed surface file