Hi,

I am trying to mask a label on top of my processed data after running TBSS based on the DTI protocol.

The issue I am having is that, it can't read anything. The data seems to be fine so my question is,

does converting using dcm2niix differ with dcm2nii when it comes to headers and would that influence the masking of labels as it is unable to get information from my processed skeleton images?

Thank you in advance!

Development of dcm2nii ended in 2016, so it predates BIDS sidecars and enhanced DICOM. If dcm2nii is able to convert your data, it should yield similar results to dcm2niix. I would suggest you try a dataset from the https://open.win.ox.ac.uk/pages/fslcourse/website/ fsl course and check your methods. The fsl jiscmail list is generally responsive to users questions.