the json extraction worked with:
“mrconvert C.mif C.nii -json_export C_Header.json”
Then I do the SPM scaling and import the json again, while converting back to mif.
But I have 3 Warnings:
[WARNING] User-defined phase-encoding direction design does not match what is stored in DWI image header; proceeding with user specification
dwifslpreproc: [WARNING] User-defined phase-encoding direction design does not match what is stored in SE EPI image header; proceeding with user specification
–> In the *.mif its “j-” after mrconvert (nothing else) its only “j” could be a bug or is it intention
[WARNING] DW gradients not correctly reoriented
–> I did not change anything with the DW Gradients or any orientation
[WARNING] filtering has reached quantisation error but desired termination criterion has not been met;
tcksift: [WARNING] disabling cost function quantisation check
(1) For number one I noticed, that if I export json and import the json… it switches between j and -j ! Is there a reason? How can I fix it?
The other ones are not clear to me. I looke dinto the nii header and the transformation matrix does not change a bit with SPM.