interfaces.semtools.brains.segmentation¶
BRAINSTalairach¶
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 string)
Additional parameters to the command
flag: %s
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
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: ('stream' or 'allatonce' or 'file' or '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¶
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 string)
Additional parameters to the command
flag: %s
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
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: ('stream' or 'allatonce' or 'file' or '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¶
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 string)
Additional parameters to the command
flag: %s
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
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: ('stream' or 'allatonce' or 'file' or '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