Hi MRTrix community =)
I am a beginner when it comes to analysing MRI, and I’d like to ask you guys some questions. A colleague has tasked me to produce some NIFTI files from 2dseqs using Nanconvert, and so I did. I now have the .nii, .bval and .bvec files for all the animals I need to analyse.
I used one of the .nii files she previously converted and explored it to check that orientations and bvals/bvecs of the files I produced are correct, however the orientation of the ones I created are incorrect (see pictures of the one she made [proper orientation] vs the one I made [all over the place]).
She had a look at the data and said the bvals and bvecs were ok despite the orientation, and that I could correct the orientation using mrtransform or mrconvert. I have read the documentation regarding both and I’m still unsure which one should I use and why. May I ask some questions?
-Which function would you use to change the orientations of the files to make the “distorted” one looking like the one she made?
-How do I check the bvals and bvecs have not been messed up with this reorientation?
-The examples in the documentation all use a .mif file (which according to my colleague contain the bvals and bvecs embedded in the file itself). This means I’ll first have to create the .nii files. Would this command work?
mrconvert -fslgrad file.bvec file.bval file.nii out.mif
-I presume I need to create the .mif files before the reorientation, right?