Difference between revisions of "DWIConvert Training Resources"
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[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DWIConverter DWIConverter Documentation] | [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DWIConverter DWIConverter Documentation] | ||
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| + | Parameters of the Slicer4.3 version | ||
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| + | *Common Parameters: Parameters used in all modes | ||
| + | *Input DWI volume file (inputVolume): Input DWI volume -- not used for DicomToNrrd mode. | ||
| + | *Output Filename (outputVolume): Output filename (.nhdr or .nrrd) | ||
| + | *Output fMRI file (fMRIOutput): Output a NRRD file, but without gradients | ||
| + | *DicomToNrrd Parameters: Parameters for Dicom to NRRD Conversion | ||
| + | *Input Dicom Data (inputDicomDirectory): Directory holding Dicom series | ||
| + | *Output Directory (outputDirectory): Directory holding the output NRRD file | ||
| + | *Gradient Vector File (gradientVectorFile): Text file giving gradient vectors | ||
| + | *Small Gradient Threshold (smallGradientThreshold): If a gradient magnitude is greater than 0 and less than smallGradientThreshold, then DWIConvert will display an error message and quit, unless the useBMatrixGradientDirections option is set. | ||
| + | Output Options: Options to control the output. | ||
| + | Write Protocol Gradients File (writeProtocolGradientsFile): 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. | ||
| + | Use Identity Measurement Frame (useIdentityMeaseurementFrame): Adjust all the gradients so that the measurement frame is an identity matrix. | ||
| + | Use BMatrix Gradient Directions (useBMatrixGradientDirections): Fill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data. In some cases the standard public gradients are not properly computed. The gradients can emperically computed from the private BMatrix fields. In some cases the private BMatrix is consistent with the public grandients, but not in all cases, when it exists BMatrix is usually most robust. | ||
| + | FSLToNrrd Parameters: FSLToNrrd Parameters | ||
| + | B Values File (inputBValues): B Values text file | ||
| + | B Vector File (inputBVectors): B Vector text file | ||
| + | NrrdToFSL Parameters: NrrdToFSL Parameters | ||
| + | B Values File (outputBValues): B Values text file | ||
| + | B Vector File (outputBVectors): B Vector text fil | ||
Revision as of 14:24, 18 June 2014
Home < DWIConvert Training ResourcesParameters of the Slicer4.3 version
- Common Parameters: Parameters used in all modes
- Input DWI volume file (inputVolume): Input DWI volume -- not used for DicomToNrrd mode.
- Output Filename (outputVolume): Output filename (.nhdr or .nrrd)
- Output fMRI file (fMRIOutput): Output a NRRD file, but without gradients
- DicomToNrrd Parameters: Parameters for Dicom to NRRD Conversion
- Input Dicom Data (inputDicomDirectory): Directory holding Dicom series
- Output Directory (outputDirectory): Directory holding the output NRRD file
- Gradient Vector File (gradientVectorFile): Text file giving gradient vectors
- Small Gradient Threshold (smallGradientThreshold): If a gradient magnitude is greater than 0 and less than smallGradientThreshold, then DWIConvert will display an error message and quit, unless the useBMatrixGradientDirections option is set.
Output Options: Options to control the output. Write Protocol Gradients File (writeProtocolGradientsFile): 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. Use Identity Measurement Frame (useIdentityMeaseurementFrame): Adjust all the gradients so that the measurement frame is an identity matrix. Use BMatrix Gradient Directions (useBMatrixGradientDirections): Fill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data. In some cases the standard public gradients are not properly computed. The gradients can emperically computed from the private BMatrix fields. In some cases the private BMatrix is consistent with the public grandients, but not in all cases, when it exists BMatrix is usually most robust. FSLToNrrd Parameters: FSLToNrrd Parameters B Values File (inputBValues): B Values text file B Vector File (inputBVectors): B Vector text file NrrdToFSL Parameters: NrrdToFSL Parameters B Values File (outputBValues): B Values text file B Vector File (outputBVectors): B Vector text fil
