open-discussion
open-discussion > RE: DTIPrep Error with Default Protocol (Bad DWI)
Jun 17, 2019 06:06 PM | Martin Styner
RE: DTIPrep Error with Default Protocol (Bad DWI)
Hi Hayley
The generic DICOM importer in Slicer does not work well for DWI data. You need to use the DWIConverter module to import your data (see also the QC presentation here (lesson 3 - slide 7) https://www.med.unc.edu/psych/research/niral/download/download-documents/)
The use of DWIConverter in Slicer is a bit clunky, but it's worth using it. On linux you can also use it on the command line:
Slicer --launch DWIConvert -i yourDicomDirectory -o yourOutput.nrrd --useBMatrixGradientDirections
(the last option is not necessary, but provides more accurate b-values and gradient vectors if the BMatrix is stored in the DICOM tags).
Best
Martin
Originally posted by Hayley Clocksin:
The generic DICOM importer in Slicer does not work well for DWI data. You need to use the DWIConverter module to import your data (see also the QC presentation here (lesson 3 - slide 7) https://www.med.unc.edu/psych/research/niral/download/download-documents/)
The use of DWIConverter in Slicer is a bit clunky, but it's worth using it. On linux you can also use it on the command line:
Slicer --launch DWIConvert -i yourDicomDirectory -o yourOutput.nrrd --useBMatrixGradientDirections
(the last option is not necessary, but provides more accurate b-values and gradient vectors if the BMatrix is stored in the DICOM tags).
Best
Martin
Originally posted by Hayley Clocksin:
Hi Martin,
I have been importing the DICOM files through Slicer, loading the relevant files and then saving them as a NRRD file. The header file specifies 25 gradients and 25 volumes.
Thank you for your help!
Hayley
I have been importing the DICOM files through Slicer, loading the relevant files and then saving them as a NRRD file. The header file specifies 25 gradients and 25 volumes.
Thank you for your help!
Hayley
Threaded View
| Title | Author | Date |
|---|---|---|
| Hayley Clocksin | Jun 14, 2019 | |
| Martin Styner | Jun 16, 2019 | |
| Hayley Clocksin | Jun 17, 2019 | |
| Martin Styner | Jun 17, 2019 | |
| Hayley Clocksin | Jun 18, 2019 | |