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