interfaces.semtools.brains.segmentation¶
BRAINSTalairach¶
Wraps the executable 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:
[Optional]
AC: (a list of items which are a float)
Location of AC Point
argument: ``--AC %s``
ACisIndex: (a boolean)
AC Point is Index
argument: ``--ACisIndex ``
PC: (a list of items which are a float)
Location of PC Point
argument: ``--PC %s``
PCisIndex: (a boolean)
PC Point is Index
argument: ``--PCisIndex ``
SLA: (a list of items which are a float)
Location of SLA Point
argument: ``--SLA %s``
SLAisIndex: (a boolean)
SLA Point is Index
argument: ``--SLAisIndex ``
IRP: (a list of items which are a float)
Location of IRP Point
argument: ``--IRP %s``
IRPisIndex: (a boolean)
IRP Point is Index
argument: ``--IRPisIndex ``
inputVolume: (a pathlike object or string representing an existing
file)
Input image used to define physical space of images
argument: ``--inputVolume %s``
outputBox: (a boolean or a pathlike object or string representing a
file)
Name of the resulting Talairach Bounding Box file
argument: ``--outputBox %s``
outputGrid: (a boolean or a pathlike object or string representing a
file)
Name of the resulting Talairach Grid file
argument: ``--outputGrid %s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a 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', nipype default value: {})
Environment variables
Outputs:
outputBox: (a pathlike object or string representing an existing
file)
Name of the resulting Talairach Bounding Box file
outputGrid: (a pathlike object or string representing an existing
file)
Name of the resulting Talairach Grid file
BRAINSTalairachMask¶
Wraps the executable 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:
[Optional]
inputVolume: (a pathlike object or string representing an existing
file)
Input image used to define physical space of resulting mask
argument: ``--inputVolume %s``
talairachParameters: (a pathlike object or string representing an
existing file)
Name of the Talairach parameter file.
argument: ``--talairachParameters %s``
talairachBox: (a pathlike object or string representing an existing
file)
Name of the Talairach box file.
argument: ``--talairachBox %s``
hemisphereMode: ('left' or 'right' or 'both')
Mode for box creation: left, right, both
argument: ``--hemisphereMode %s``
expand: (a boolean)
Expand exterior box to include surface CSF
argument: ``--expand ``
outputVolume: (a boolean or a pathlike object or string representing
a file)
Output filename for the resulting binary image
argument: ``--outputVolume %s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a 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', nipype default value: {})
Environment variables
Outputs:
outputVolume: (a pathlike object or string representing an existing
file)
Output filename for the resulting binary image
SimilarityIndex¶
Wraps the executable 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:
[Optional]
outputCSVFilename: (a pathlike object or string representing an
existing file)
output CSV Filename
argument: ``--outputCSVFilename %s``
ANNContinuousVolume: (a pathlike object or string representing an
existing file)
ANN Continuous volume to be compared to the manual volume
argument: ``--ANNContinuousVolume %s``
inputManualVolume: (a pathlike object or string representing an
existing file)
input manual(reference) volume
argument: ``--inputManualVolume %s``
thresholdInterval: (a float)
Threshold interval to compute similarity index between zero and one
argument: ``--thresholdInterval %f``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a 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', nipype default value: {})
Environment variables
Outputs:
None