DWIConvert Training Resources

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DWIConverter Documentation

Parameters of the Slicer4.3.1 version

• Conversion Options: Options 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)
• Dicom To NiftiNrrd Conversion: Parameters for Dicom to NRRD Conversion
• Input Dicom Data (inputDicomDirectory): Directory holding Dicom series
• Output Directory (outputDirectory): Directory holding the output NRRD file
• NiftiFSL To Nrrd Conversion: FSLToNrrd Parameters
• Input BVals File (inputBValues): B Values text file
• Input BVec File (inputBVectors): B Vector text file
• Nrrd To NiftiFSL COnversion: NrrdToFSL Parameters
• Output BVals File (outputBValues): B Values text file
• Output BVec File (outputBVectors): B Vector text file
• Advanced Conversion Options
• Output fMRI file (fMRIOutput): Output a NRRD file, but without gradients
• 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 protocol 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.

Description of different sections:

1. Output OPtions:

‹writeProtocolGradientsFile ‹ writes the DWI gradient vectors as a simple text file, used for debugging.

‹useIdentityMeasurementFrame ‹ more complicated: There are two reference frames with respect to DWI file. There¹s the image reference frame, which defines the patient position and orientation for the gradient magnitude voxel grid, and there is a measurement frame, which is the reference frame of the gradient vectors. This flag modifies the gradients written out so that they are in the Image reference frame.

‹useBMatrixGradientDirections From DWIConvert ‹help output: 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 empirically 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.

In other words, the Siemens data includes both a Bmatrix tag, and an explicit set of gradient vectors. For some DWI datasets, the scanner puts incorrect data in the explicit gradients, but the correct gradients can be recovered by computations on the Bmatrix. This option selects the latter method.

2. The manufacturers supported are Siemens, Philips, GE and Hitachi. The Hitachi support is experimental,as it has only been tested with scans from one site.

3. ‹fMRIOutput ‹ this outputs a NRRD file, but doesn¹t include gradient vectors. It would be used if you were interested in converting functional MRI datasets, instead of DWI datasets.

4. Nifti is a revised version of the Analyze format where the header and pixel data are usually merged into a single ".nii" file. The Nifti format stores the orientation of the image volume in two ways: one, using both the rotation and translation in order to map the voxel coordinates to the specific scanner's frame of reference, the second method saves the general linear transformation to change the alignment of the image volume to a more standard coordinate system. (Larobina M, Murino L: Medical Image File Formats. J Digit Imaging (2014) 27:200-206)

Conversion from the Command Line

• Slicer build

NrrdToFSL: /Applications/Slicer.app/Contents/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/EAAG_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/EAAG_vtkMRMLDiffusionWeightedVolumeNodeC.nrrd --inputDicomDirectory . --outputBValues bval --outputBVectors bvec --outputDirectory . --smallGradientThreshold 0.2

• Slicer executable

NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ~/Desktop/test/dwi1.nhdr --outputVolume ~/Desktop/test/dwi1_fsl.nii.gz --outputBValues ~/Desktop/test/bvals.txt --outputBVectors ~/Desktop/test/bvec.txt FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ~/Desktop/test/dwi1_fsl.nii.gz --outputVolume ~/Desktop/test/dwi1_reconverted.nrrd --inputBValues ~/Desktop/test/bvals.txt --inputBVectors ~/Desktop/test/bvec.txt