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# interfaces.semtools.brains.segmentation

## BRAINSTalairach

Link to code

Wraps command ** BRAINSTalairach **

title: BRAINS Talairach

category: BRAINS.Segmentation

description: This program creates a VTK structured grid defining the Talairach coordinate system based on four points: AC, PC, IRP, and SLA. The resulting structred grid can be written as either a classic VTK file or the new VTK XML file format. Two representations of the resulting grid can be written. The first is a bounding box representation that also contains the location of the AC and PC points. The second representation is the full Talairach grid representation that includes the additional rows of boxes added to the inferior allowing full coverage of the cerebellum.

version: 0.1

documentation-url: http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSTalairach

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: Steven Dunn and Vincent Magnotta

acknowledgements: Funding for this work was provided by NIH/NINDS award NS050568

Inputs:

    [Mandatory]

    [Optional]
    AC: (a list of items which are a float)
            Location of AC Point
            flag: --AC %s
    ACisIndex: (a boolean)
            AC Point is Index
            flag: --ACisIndex
    IRP: (a list of items which are a float)
            Location of IRP Point
            flag: --IRP %s
    IRPisIndex: (a boolean)
            IRP Point is Index
            flag: --IRPisIndex
    PC: (a list of items which are a float)
            Location of PC Point
            flag: --PC %s
    PCisIndex: (a boolean)
            PC Point is Index
            flag: --PCisIndex
    SLA: (a list of items which are a float)
            Location of SLA Point
            flag: --SLA %s
    SLAisIndex: (a boolean)
            SLA Point is Index
            flag: --SLAisIndex
    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
    inputVolume: (an existing file name)
            Input image used to define physical space of images
            flag: --inputVolume %s
    outputBox: (a boolean or a file name)
            Name of the resulting Talairach Bounding Box file
            flag: --outputBox %s
    outputGrid: (a boolean or a file name)
            Name of the resulting Talairach Grid file
            flag: --outputGrid %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:

    outputBox: (an existing file name)
            Name of the resulting Talairach Bounding Box file
    outputGrid: (an existing file name)
            Name of the resulting Talairach Grid file

## BRAINSTalairachMask

Link to code

Wraps command ** BRAINSTalairachMask **

title: Talairach Mask

category: BRAINS.Segmentation

description: This program creates a binary image representing the specified Talairach region. The input is an example image to define the physical space for the resulting image, the Talairach grid representation in VTK format, and the file containing the Talairach box definitions to be generated. These can be combined in BRAINS to create a label map using the procedure Brains::WorkupUtils::CreateLabelMapFromBinaryImages.

version: 0.1

documentation-url: http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSTalairachMask

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: Steven Dunn and Vincent Magnotta

acknowledgements: Funding for this work was provided by NIH/NINDS award NS050568

Inputs:

    [Mandatory]

    [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
    expand: (a boolean)
            Expand exterior box to include surface CSF
            flag: --expand
    hemisphereMode: ('left' or 'right' or 'both')
            Mode for box creation: left, right, both
            flag: --hemisphereMode %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
    inputVolume: (an existing file name)
            Input image used to define physical space of resulting mask
            flag: --inputVolume %s
    outputVolume: (a boolean or a file name)
            Output filename for the resulting binary image
            flag: --outputVolume %s
    talairachBox: (an existing file name)
            Name of the Talairach box file.
            flag: --talairachBox %s
    talairachParameters: (an existing file name)
            Name of the Talairach parameter file.
            flag: --talairachParameters %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:

    outputVolume: (an existing file name)
            Output filename for the resulting binary image

## SimilarityIndex

Link to code

Wraps command ** SimilarityIndex **

title: BRAINSCut:SimilarityIndexComputation

category: BRAINS.Segmentation

description: Automatic analysis of BRAINSCut Output

version: 1.0

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: Eunyoung Regin Kim

Inputs:

    [Mandatory]

    [Optional]
    ANNContinuousVolume: (an existing file name)
            ANN Continuous volume to be compared to the manual volume
            flag: --ANNContinuousVolume %s
    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
    inputManualVolume: (an existing file name)
            input manual(reference) volume
            flag: --inputManualVolume %s
    outputCSVFilename: (an existing file name)
            output CSV Filename
            flag: --outputCSVFilename %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
    thresholdInterval: (a float)
            Threshold interval to compute similarity index between zero and one
            flag: --thresholdInterval %f

Outputs:

    None