Diffusion brain: DICOM to NRRD conversion

Operating system: MacOS
Slicer version: 4.11

I am having little difficulty in converting the Dicom images to NRRD using DWIConvert. I believe something is not happening correctly during conversion as after conversion I can’t find any DWI components to choose. I am uploading the 24 sequences of DWI in Dicom. I can also upload the Dicom header info if anyone requires.

Any help will be really appreciated.

You might want to choose the Extension Manager menu item from the View menu and install the SlicerDcm2nii module.@ihnorton can provide more details. This will give you access to the DCM2niixGUI module where you can select an input folder and apply.

There are two other options:

  1. Use dcm2niix from the command line. Provide the -e y to export to NRRD (instead of NIfTI), so the minimal command line would be dcm2niix -e y /path/to/DICOMs
  2. Get MRIcroGL and choose Convert DICOM to NIfTI from the Import menu. This provides a nice graphical wrapper for the many options available with dcm2niix. The relevant one for you is to choose NRRD from the Output Format drop down.

If you continue having issues, you may want to provide details regarding the scanner manufacturer (e.g. Bruker, Canon, GE, Philips, Siemens, UIH), as they each use different methods to define DTI parameters.

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@Chris_Rorden Thank you for your response. But its not working still. I can post the dicom headers, if that helps.

@Chris_Rorden I sent you a google drive link with my data.

@rahulpaul your DICOM images are from a Siemens VB17 MRI system. Unfortunately, the images were overzealously anonymized, removing the crucial sequence details stored in the CSA header. The gradient directions and many other parameters are stored in the CSA header. Without these details, it is impossible for any conversion tool to infer these properties. I suggest you check the provenance of these images. Images directly from the scanner will have the CSA header intact, and you need to chose an anonymization tool that preserves this. This is a limitation of your images, not the tools used to import DICOM data.