I am currently preprocessing an fMRI dataset and ran into an error with mtnormalise that seems to be different to the ones here discussed.
The program fails with:
mtnormalise: [ERROR] Non-positive tissue balance factor was computed. Balance factors: -nan -nan -nan
While checking the steps before, I realized that the gmfod.mif is nearly plain white as it can be seen on the image.
Hence, vf.mif does not contain grey matter at all. This seemed quite strange to me, as wmfod.mif and csffod.mif look quite normal.
is there anything wrong in my >dwi2fod< ?
dwifslpreproc 64_dir_den.mif 64_den_preproc.mif -nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options " --slm=linear --data_is_shelled" dwibiascorrect ants 64_den_preproc.mif 64_den_preproc_unbiased.mif -bias bias.mif -force dwi2mask 64_den_preproc_unbiased.mif mask.mif dwi2response dhollander 64_den_preproc_unbiased.mif wm.txt gm.txt csf.txt -voxels voxels.mif dwi2fod msmt_csd 64_den_preproc_unbiased.mif -mask mask.mif wm.txt wmfod.mif gm.txt gmfod.mif csf.txt csffod.mif
I am quite new to MRtrix so I don’t know if I missed something obvious here, any help and comments are very welcome!