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# nipype.interfaces.semtools.brains.segmentation module

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## BRAINSTalairach

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `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

> ACa list of items which are a float

>   Location of AC Point . Maps to a command-line argument: `--AC %s`.

> ACisIndexa boolean

>   AC Point is Index. Maps to a command-line argument: `--ACisIndex`.

> IRPa list of items which are a float

>   Location of IRP Point . Maps to a command-line argument: `--IRP %s`.

> IRPisIndexa boolean

>   IRP Point is Index. Maps to a command-line argument: `--IRPisIndex`.

> PCa list of items which are a float

>   Location of PC Point . Maps to a command-line argument: `--PC %s`.

> PCisIndexa boolean

>   PC Point is Index. Maps to a command-line argument: `--PCisIndex`.

> SLAa list of items which are a float

>   Location of SLA Point . Maps to a command-line argument: `--SLA %s`.

> SLAisIndexa boolean

>   SLA Point is Index. Maps to a command-line argument: `--SLAisIndex`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputVolumea pathlike object or string representing an existing file

>   Input image used to define physical space of images. Maps to a command-line argument: `--inputVolume %s`.

> outputBoxa boolean or a pathlike object or string representing a file

>   Name of the resulting Talairach Bounding Box file. Maps to a command-line argument: `--outputBox %s`.

> outputGrida boolean or a pathlike object or string representing a file

>   Name of the resulting Talairach Grid file. Maps to a command-line argument: `--outputGrid %s`.

> outputBoxa pathlike object or string representing an existing file

>   Name of the resulting Talairach Bounding Box file.

> outputGrida pathlike object or string representing an existing file

>   Name of the resulting Talairach Grid file.

## BRAINSTalairachMask

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `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

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> expanda boolean

>   Expand exterior box to include surface CSF. Maps to a command-line argument: `--expand`.

> hemisphereMode‘left’ or ‘right’ or ‘both’

>   Mode for box creation: left, right, both. Maps to a command-line argument: `--hemisphereMode %s`.

> inputVolumea pathlike object or string representing an existing file

>   Input image used to define physical space of resulting mask. Maps to a command-line argument: `--inputVolume %s`.

> outputVolumea boolean or a pathlike object or string representing a file

>   Output filename for the resulting binary image. Maps to a command-line argument: `--outputVolume %s`.

> talairachBoxa pathlike object or string representing an existing file

>   Name of the Talairach box file. Maps to a command-line argument: `--talairachBox %s`.

> talairachParametersa pathlike object or string representing an existing file

>   Name of the Talairach parameter file. Maps to a command-line argument: `--talairachParameters %s`.

> outputVolumea pathlike object or string representing an existing file

>   Output filename for the resulting binary image.

## SimilarityIndex

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `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

> ANNContinuousVolumea pathlike object or string representing an existing file

>   ANN Continuous volume to be compared to the manual volume. Maps to a command-line argument: `--ANNContinuousVolume %s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputManualVolumea pathlike object or string representing an existing file

>   Input manual(reference) volume. Maps to a command-line argument: `--inputManualVolume %s`.

> outputCSVFilenamea pathlike object or string representing an existing file

>   Output CSV Filename. Maps to a command-line argument: `--outputCSVFilename %s`.

> thresholdIntervala float

>   Threshold interval to compute similarity index between zero and one. Maps to a command-line argument: `--thresholdInterval %f`.