How to view FODs in two shell/tissue data

I have dwi data with b=0,1000 and following the BATMAN tutorial, I noticed the FODs seem correct but the color coding of tissue types is missing.

My commands:

dwi2response dhollander ${dir_out_sub}/dwi_${subject}_preproc_unbias.mif response_wm_${subject}.txt response_gm_${subject}.txt response_csf_${subject}.txt -voxels voxels_${subject}.mif -force

dwi2fod msmt_csd ${dir_out_sub}/dwi_${subject}_preproc_unbias.mif response_wm_${subject}.txt wmfod_${subject}.mif response_csf_${subject}.txt csffod_${subject}.mif -mask ${dir_out_sub}/dwi_${subject}_mask.mif -force

mrconvert -coord 2 0 wmfod_${subject}.mif -| mrcat csffod_${subject}.mif - vf_${subject}.mif -force

Then to view I write:
ds: mrview vf_${subject}.mif -odf.load_sh wmfod_${subject}.mif

Is there something I am missing or is it just not possible to view the tissue color segmentation like so:


1 Like

For mrview to display RGB images, there have to be 3 volumes in your mif file and your image has just 2.

With your current mif file, you can simply use the left-right arrow keys to switch between the tissue types.

If you want to see them together in an RGB image, you will have to add an extra channel containing just zeros, e.g.:

mrcat csffod_${subject}.mif $(mrcalc csffod_${subject}.mif 0 -multiply -) $(mrconvert -coord 2 0 wmfod_${subject}.mif -) vf_${subject}.mif -force