How to average FODs

[mschira]

Hi
I have several DWI scans from the same subject and I want to combine these on the FOD level.
I have successfully aligned all the scans using ANTs and I have applied the ANTs nonlinear transforms successfully to the FOD images.

Registration: using transformations generated from other packages

The mrtransform allows the spatial transformation of images when provided with a suitable linear or nonlinear transformation (“warp”). For linear transformations, MRtrix3 uses homogeneous transformation matrices stored as plain text. These can be converted from FSL and ITK-based (plain text) convention with the command transformconvert. The MRtrix3 tools expect nonlinear transformations in an image format where each voxel defines the scanner space location in the other image. This transformatio…

I have tested this, by estimating a DEC using fod2dec from the warped_fod,mif and DEC aligns with the template.

So essentially, I now have several fod images in the exact same voxel space and I need to make an “average” (or combined) FOD.

What’s the right approach to do this? Can I just make an average?
Using mrcalc?
I can’t see a -average command? use -add and -divide?
M.

[maxpietsch]

FODs can be averaged voxel-wise via the tool mrmath.

[mschira]

Thanks,
voxelwise average, too easy.
Though I think mrcalc does that?
Anyway, can do.
M.

[rsmith]

voxelwise average, too easy.
Though I think mrcalc does that?

While mrcalc could do it, it would involve a whole lot of ... image1.mif -add image2.mif -add ....
mrmath not only doesn’t require you to keep specifying -add in between each pair, but also to use e.g. the wildcard character to grab many images with fewer keystrokes.