DWI Converter error - how to convert NRRD to FSL?

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DWI Converter error - how to convert NRRD to FSL?

MeganS
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Hello,
 
I am having some problems converting the output of DTIPrep .nrrd file into FSL format.
 
In the 3D Slicer, DWI Convert I get the following error log:
 
Found CommandLine Module, target is /Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert
ModuleType: CommandLineModule
DWIConverter command line:
 
/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --inputDicomDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --outputBValues /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvals.bval --outputBVectors /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvecs.bvec --outputDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --smallGradientThreshold 0.2
 
 
DWIConverter standard error:
 
Error: ReadVolume: Unsupported source pixel type.
Input volume: unsigned_short
Output volume: short
The only supported output type is <short>. You may consider using allowLossyConversion option.
However, use this option with caution! Conversion from images of a different type may cause data loss due to rounding or truncation.
 
 
DWIConverter standard error:
 
Error: ReadVolume: Unsupported source pixel type.
Input volume: unsigned_short
Output volume: short
The only supported output type is <short>. You may consider using allowLossyConversion option.
However, use this option with caution! Conversion from images of a different type may cause data loss due to rounding or truncation.
 
DWIConverter completed with errors
 
 
Found CommandLine Module, target is /Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert
ModuleType: CommandLineModule
DWIConverter command line:
 
/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeD.nrrd --inputDicomDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --outputBValues /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvals.bval --outputBVectors /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvecs.bvec --outputDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --smallGradientThreshold 0.2
 
 
DWIConverter standard error:
 
Error: ReadVolume: Unsupported source pixel type.
Input volume: unsigned_short
Output volume: short
The only supported output type is <short>. You may consider using allowLossyConversion option.
However, use this option with caution! Conversion from images of a different type may cause data loss due to rounding or truncation.
 
 
 
DWIConverter completed with errors
 
 
Found CommandLine Module, target is /Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert
ModuleType: CommandLineModule
 
DWIConverter command line:
 
/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeD.nrrd --inputDicomDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --outputBValues /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvals.bval --outputBVectors /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvecs.bvec --outputDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --smallGradientThreshold 0.2
 
 
DWIConverter standard error:
 
Error: ReadVolume: Unsupported source pixel type.
Input volume: unsigned_short
Output volume: short
The only supported output type is <short>. You may consider using allowLossyConversion option.
However, use this option with caution! Conversion from images of a different type may cause data loss due to rounding or truncation.
 
DWIConverter completed with errors
 
 
 
 
I checked the “Lossy Conversion” option and it ran with no errors, but my output files that were saved included the .bvec and .bval file but not NIFTI file.
 
I’m not sure what I am doing wrong. Any help is much appreciated.
 
Thanks,
 
Megan