nipype.interfaces.semtools.brains.segmentation module¶
Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.
BRAINSTalairach¶
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 structured 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
- Optional Inputs:
AC (a list of items which are a float) – Location of AC Point . Maps to a command-line argument:
--AC %s.ACisIndex (a boolean) – AC Point is Index. Maps to a command-line argument:
--ACisIndex.IRP (a list of items which are a float) – Location of IRP Point . Maps to a command-line argument:
--IRP %s.IRPisIndex (a boolean) – IRP Point is Index. Maps to a command-line argument:
--IRPisIndex.PC (a list of items which are a float) – Location of PC Point . Maps to a command-line argument:
--PC %s.PCisIndex (a boolean) – PC Point is Index. Maps to a command-line argument:
--PCisIndex.SLA (a list of items which are a float) – Location of SLA Point . Maps to a command-line argument:
--SLA %s.SLAisIndex (a boolean) – SLA Point is Index. Maps to a command-line argument:
--SLAisIndex.args (a string) – Additional parameters to the command. Maps to a command-line 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’) – Environment variables. (Nipype default value:
{})inputVolume (a 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.outputBox (a 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.outputGrid (a 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.- 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¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line 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’) – Environment variables. (Nipype default value:
{})expand (a 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.inputVolume (a 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.outputVolume (a 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.talairachBox (a pathlike object or string representing an existing file) – Name of the Talairach box file. Maps to a command-line argument:
--talairachBox %s.talairachParameters (a pathlike object or string representing an existing file) – Name of the Talairach parameter file. Maps to a command-line argument:
--talairachParameters %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Output filename for the resulting binary image.
SimilarityIndex¶
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
- Optional Inputs:
ANNContinuousVolume (a 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.args (a string) – Additional parameters to the command. Maps to a command-line 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’) – Environment variables. (Nipype default value:
{})inputManualVolume (a pathlike object or string representing an existing file) – Input manual(reference) volume. Maps to a command-line argument:
--inputManualVolume %s.outputCSVFilename (a pathlike object or string representing an existing file) – Output CSV Filename. Maps to a command-line argument:
--outputCSVFilename %s.thresholdInterval (a float) – Threshold interval to compute similarity index between zero and one. Maps to a command-line argument:
--thresholdInterval %f.