A warning in the fixel pipeline


I am building a pipeline to run multi-tissue CSD on a dataset. When I create the FD metric for each subject it seems like they inherit the transformation matrix header from the original FOD image (I am using the duplicates of the same subject for now just to test the pipeline). However, when I create the FC metric from the warps their transform matrices are assigned identity matrices. As a result of this at the FD*FC stage to calculate FDC I am getting a warning related to this matrix mismatch. It looks like the FD and FC aligns okay when I overlay them. Could this warning be ignored in this case? I am also attaching a screenshot of the headers.


Hi Ozzy,

These are fixel data files, and as such their transforms are completely ignored – it doesn’t matter if they differ. The only image whose transform is taken into account is the corresponding index image. Please take a look through the documentation for the fixel format to understand why that is. Hopefully that’ll make sense, but feel free to ask again if it doesn’t.

All the best,