I realize I am very late with this reply, my apologies. I got caught up in longitudinal data collection for my project followed by analyses of the collected behavioral data, and this post slipped my mind. Anyway, better late than never, and maybe it could still help others .
I figured out how to open the FA color images created by MRtrix (tensor2metric -vector) in:
- ITK-snap: tools > layer inspector > general > display mode > RGB display
- fsleyes: change 3D/4D volume (top left) to 3-direction vector image (RGB)
- Freeview: file > load DTI volume > load fa.nii (from tensor2metric -fa) as FA data file and dec.nii (from tensor2metric -vec) as DTI vector file
- mricron/mricroGL: open FA image as main image and then iteratively add the 3 different volumes of the dec.nii as an overlay image (overlay > add), adjust the color scale of the first overlay to red, the second one to green and the third one to blue.
The image intensities in dec.nii can indeed be negative or above 1 in my case. Although the “raw” dec.nii image still opens in the programs listed above as is, it looks indeed more familiar to me after taking the absolute values of the image values using
mrcalc -abs (as discussed in this post) and suggested by Thijs.
However, I still cannot open the image in Trackvis (which is the software I actually want to use ), also not with the trick of inserting the extra singleton dimension along the 4th axis. I have previously used Trackvis with FAC images created by ExploreDTI. It turns out ExploreDTI creates a 3D RGB24 image instead of a 4D image with three volumes. So Thijs was correct in that it probably doesn’t open 4D images… Do you think I can obtain such 3D RGB24 images somehow in MRtrix, or should I go through the pipeline in ExploreDTI?
Thank you, and, if you happen to reply in 2 years like I did, I totally understand