The fixel2sh was executed in this subject and the SH result (sagittal view) was displayed in the same view.
The data being shown in the corresponding screenshot were produced by the fixel tool, but the output of the fixel2sh command is an SH series, which should be displayed using the ODF tool. It might be useful to be able to see those intermediate data to know where the problem first originates.
I don’t understand why there exist the different orientation (Can I call it that?) in final sh2peaks result compared with the WM-FOD or FD result.
Neither do I. These kinds of orientation flips can happen, e.g. converting between formats, but not normally in a subset of the image like that. I did a quick sanity check that that sequence of commands doesn’t cause an issue on an exemplar dataset. But I’m kind of baffled.
In addition to fixing the screenshot for the output of fixel2sh, it would be useful if you could post the exact commands that were used to generate the final result.
(If you’ve used the .mif format throughout, you could run mrinfo -property command_history on the output of sh2peaks and post the relevant content here)
