DTI Analysis using Nifti file

Hello Everyone,

I am working with the .nii files to perform the DTI analysis and the .nii images are converted from Bruker file using Matlab. The problem I am facing is when using the Volumes module the software is not able to detect the diffusion component to select different components (the file format used: 4D nifti with 4th dimension as the 11 images from B0 to B10). I’d really appreciate if anyone can help with the issue I am facing. I can send a link to the file if required.

If it is not possible to use the .nii files for DTI analysis in Slicer then is there a way to convert Bruker file to .nrrd?

You can try the SlicerDMRI DWIConvert module for nifti to nrrd. Another option is if you have bruker DICOM, the dcm2nii program can now output nrrd files.

I think you will need to work with Bruker for a solution. Last I checked, there were two errors in the Bruker DWI DICOM files that made them unsuitable for analysis.

  1. The DICOM public tags are supposed to store [xx,xy,xz,yy,yz,zz], but Bruker has saved [xx,xy,xz,yx,yy,yz]. Unfortunately, you can not reconstruct the B-matrix from this.
  2. Second, they only provide the B-Matrix, not the gradient vector. While the vector [1,0,0] and [-1,0,0] generate the same B-matrix, they have different eddy currents (which tools like FSL’s Eddy leverage).

If all of your scans were acquired with slice angulation orthogonal to the scanner bore, you can probably insert a single gradient table you can extract.

Alternatively, if you have the Bruker-format data (rather than DICOM) there may be a way to extract the gradient directions. The new ParaVision 360 should allow export to NIfTI, and you could use @tbillah’s Python conversion scripts to convert the NIfTI (with FSL bvec/bval) to NRRD format (with embedded gradient directions).

I would contact your Bruker research collaboration manager for help on this. It is a professional product and they have an obligation to stand by their DICOM conformance statement.