# DTI Analysis using Nifti file

**URL:** <https://discourse.slicer.org/t/dti-analysis-using-nifti-file/8283>\
**Category:** Support\
**Tags:** nifti, nrrd, dti\
**Created:** [September 3, 2019, 7:27pm UTC](https://discourse.slicer.org/t/dti-analysis-using-nifti-file/8283 "2019-09-03T19:27:54Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![nirav](https://avatars.discourse-cdn.com/v4/letter/n/f1d935/32.png) [@nirav](https://discourse.slicer.org/u/nirav)\
**Post date:** [September 3, 2019, 7:27pm UTC](https://discourse.slicer.org/t/dti-analysis-using-nifti-file/8283/1 "2019-09-03T19:27:54Z")

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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?

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**Author:** ![ljod](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ljod/32/652_2.png) [@ljod](https://discourse.slicer.org/u/ljod)\
**Post date:** [September 3, 2019, 8:07pm UTC](https://discourse.slicer.org/t/dti-analysis-using-nifti-file/8283/2 "2019-09-03T20:07:42Z")

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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.

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**Author:** ![Chris\_Rorden](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chris_rorden/32/4073_2.png) [@Chris\_Rorden](https://discourse.slicer.org/u/Chris_Rorden)\
**Post date:** [September 3, 2019, 8:13pm UTC](https://discourse.slicer.org/t/dti-analysis-using-nifti-file/8283/3 "2019-09-03T20:13:31Z")

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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](https://github.com/pnlbwh/conversion) 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](https://github.com/neurolabusc/Bru2Nii/issues/24) should allow export to NIfTI, and you could use @tbillah’s [Python conversion scripts](https://github.com/pnlbwh/conversion) 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.