nipype.interfaces.slicer.converters module¶
Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.
DicomToNrrdConverter¶
Bases: SEMLikeCommandLine
Wrapped executable:
DicomToNrrdConverter.title: DICOM to NRRD Converter
category: Converters
description: Converts diffusion weighted MR images in dicom series into Nrrd format for analysis in Slicer. This program has been tested on only a limited subset of DTI dicom formats available from Siemens, GE, and Phillips scanners. Work in progress to support dicom multi-frame data. The program parses dicom header to extract necessary information about measurement frame, diffusion weighting directions, b-values, etc, and write out a nrrd image. For non-diffusion weighted dicom images, it loads in an entire dicom series and writes out a single dicom volume in a .nhdr/.raw pair.
version: 0.2.0.$Revision: 916 $(alpha)
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DicomToNrrdConverter
license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
contributor: Xiaodong Tao (GE), Vince Magnotta (UIowa), Hans Johnson (UIowa)
acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Additional support for DTI data produced on Philips scanners was contributed by Vincent Magnotta and Hans Johnson at the University of Iowa.
- 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:
{})inputDicomDirectory (a pathlike object or string representing an existing directory) – Directory holding Dicom series. Maps to a command-line argument:
--inputDicomDirectory %s.outputDirectory (a boolean or a pathlike object or string representing a directory) – Directory holding the output NRRD format. Maps to a command-line argument:
--outputDirectory %s.outputVolume (a string) – Output filename (.nhdr or .nrrd). Maps to a command-line argument:
--outputVolume %s.smallGradientThreshold (a float) – If a gradient magnitude is greater than 0 and less than smallGradientThreshold, then DicomToNrrdConverter will display an error message and quit, unless the useBMatrixGradientDirections option is set. Maps to a command-line argument:
--smallGradientThreshold %f.useBMatrixGradientDirections (a boolean) – Fill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data. Maps to a command-line argument:
--useBMatrixGradientDirections.useIdentityMeaseurementFrame (a boolean) – Adjust all the gradients so that the measurement frame is an identity matrix. Maps to a command-line argument:
--useIdentityMeaseurementFrame.writeProtocolGradientsFile (a boolean) – Write the protocol gradients to a file suffixed by ‘.txt’ as they were specified in the procol by multiplying each diffusion gradient direction by the measurement frame. This file is for debugging purposes only, the format is not fixed, and will likely change as debugging of new dicom formats is necessary. Maps to a command-line argument:
--writeProtocolGradientsFile.- Outputs:
outputDirectory (a pathlike object or string representing an existing directory) – Directory holding the output NRRD format.
OrientScalarVolume¶
Bases: SEMLikeCommandLine
Wrapped executable:
OrientScalarVolume.title: Orient Scalar Volume
category: Converters
description: Orients an output volume. Rearranges the slices in a volume according to the selected orientation. The slices are not interpolated. They are just reordered and/or permuted. The resulting volume will cover the original volume. NOTE: since Slicer takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume, To see the difference, save the volume and display it with a system that either ignores the orientation of the image (e.g. Paraview) or displays individual images.
version: 0.1.0.$Revision: 19608 $(alpha)
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/OrientImage
contributor: Bill Lorensen (GE)
acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
- 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:
{})inputVolume1 (a pathlike object or string representing an existing file) – Input volume 1. Maps to a command-line argument:
%s(position: -2).orientation (‘Axial’ or ‘Coronal’ or ‘Sagittal’ or ‘RIP’ or ‘LIP’ or ‘RSP’ or ‘LSP’ or ‘RIA’ or ‘LIA’ or ‘RSA’ or ‘LSA’ or ‘IRP’ or ‘ILP’ or ‘SRP’ or ‘SLP’ or ‘IRA’ or ‘ILA’ or ‘SRA’ or ‘SLA’ or ‘RPI’ or ‘LPI’ or ‘RAI’ or ‘LAI’ or ‘RPS’ or ‘LPS’ or ‘RAS’ or ‘LAS’ or ‘PRI’ or ‘PLI’ or ‘ARI’ or ‘ALI’ or ‘PRS’ or ‘PLS’ or ‘ARS’ or ‘ALS’ or ‘IPR’ or ‘SPR’ or ‘IAR’ or ‘SAR’ or ‘IPL’ or ‘SPL’ or ‘IAL’ or ‘SAL’ or ‘PIR’ or ‘PSR’ or ‘AIR’ or ‘ASR’ or ‘PIL’ or ‘PSL’ or ‘AIL’ or ‘ASL’) – Orientation choices. Maps to a command-line argument:
--orientation %s.outputVolume (a boolean or a pathlike object or string representing a file) – The oriented volume. Maps to a command-line argument:
%s(position: -1).- Outputs:
outputVolume (a pathlike object or string representing an existing file) – The oriented volume.