support DWI

[grandjeanlab]

Hi.
Would it be possible to have support for DWI to get both bvec and bval, in addition to the nifti?

AFAIK:
bvals can be found under PVM_DwEffBvals in the corresponding method file for the scan.
bvec are found under PVM_DwGradRead, PVM_DwGrandPhase, and PVM_DwGradeSlice in the same file.

[neurolabusc]

Feel free to add this feature, and issue a pull request if you want to share it with others. You may also want to explore bruker2nifti which will extract a DwGradVec.txt file for you. If you are hoping to create FSL format bval and bvec files, you will want to carefully validate your solution.

• Be aware that the BMatrix is not sufficient to determine the BVector (e.g. the BVecs [-1 0 0] and [1 0 0] generate the same BMatrix).
• The FSL format bvecs are described with respect to the image plane and not the scanner bore. FSL assumes a radiological convention as noted here.
• In my experience, the orientations of Bruker images can be unexpected. I think some individuals put the animals in prone, while others put them in supine, and rodent's anterior-posterior direction is different than a primate's when in either of these positions. For a generalized approach you will want to explore this carefully. At least with DICOM there are tags for quadruped as well as prone/supine, but even those assume the operator has set them correctly.