Hi Martin,

Thank you for your response:

1. I downloaded DTIPrep version 1.2.7 from the NITRC website. I am able to input the FSL bet2 path but am not sure what paths to input for the other tools. Could you provide me with the directory paths for the other tools? When I look at the package contents I cannot tell where or what files to specify.

2. With Slicer version 4.6.2 I do not see an option to add the DTIPrep extension. If is not compatible then I assume specifying where to find the tools in the standalone version of DTIPrep is the way to go? Otherwise, what version of Slicer is compatible with DTIPrep that would allow me to add as an extension?

3/4. With the output file from DTIPrep I have been trying to figure out in Slicer how to convert the image into FSL format using the DWIConverter but receive several error message. I posted the error log on the Slicer community list but have not gotten any replies. Perhaps you could help me figure out the issue. The following is the errors I receive: 



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 . 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 . 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 . 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 . 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 no NIFTI file.

Do you have a list of steps to take to convert to NIFTI format with the pipeline you use for your FSL analyses? Originally I used DWIConverter to convert my DICOM images to NRRD. And then am trying to use the NRRD to FSL option with the output from DTIPrep.

5. I did enable the sphere and gradient display as the manual shows but there is just a blank screen when I click on 3d mode. When I switch back to MPR I see the gradient I am trying to view but then nothing when I go back to 3d view. 

One other question is about the default protocol values and how to determine whether I should use the default protocol or make any changes. A tutorial I found on the NITRC site says that more information on the default protocol is available on the site but i cannot find that information. 

I'm sorry for all the questions, I am definitely a novice with these programs and recently discovered them when I was trying to figure out how to increase reliability in longitudinal TBSS studies. 

Thank you for your help,

Megan