Hi Mrtrix experts,
I analyzed my data in diffusion space, and did whole brain tractography. Now I would like to transform my tracts to standard space. I thought I could use the tcknormalise command for this purpose, so using FSL flirt I estimated the transformation from DWI to T1 and then to MNI space. However, if I do “tcknormalise tracks_in.tck dwi2standard.nii.gz tracks_out.tck”, what I obtain is one big string of tracts, on the outside of my brain.
Did anyone of you already use this command or could somebody explain me what I’m doing wrong?