Split dwi

1

Hi all!

First, thank you very much for that fantastic application.

My problem:

I received a split dwi data set with 2x 923 images, I have no idea why it’s split.
Now I can use mrcat to combine the datasets, but then I receive 2x bvecs and 2x bvals of course.
When I want to use the command dwipreproc, the image has twice the amount of diffusion directions, so the command doesn’t work. How can I use both bvecs / bvals? Do I have to use dwipreproc for both sets before mrcat and then combine them?

I guess my question could be interesting in this topic as well.

I appreciate your help very much, best regards, Lucius

2

So the simplest here would be to convert each image to a format that can hold the DW scheme in the header (i.e. .mif), importing the relevant bvecs/bvals in the process, then using mrcat to merge them as per the topic you linked to. So this might look like:

mrconvert dwi1.nii -fslgrad bvecs1 bvals1 dwi1.mif
mrconvert dwi2.nii -fslgrad bvecs2 bvals2 dwi2.mif
mrcat dwi1.mif dwi2.mif -axis 3 dwi_all.mif

Hopefully that’ll do it…

1 Like
3

Thank you ever so much! It worked perfectly.

4

Just to expand on this slightly: The reason this works is that commands such as mrcat can read the diffusion gradient scheme from each individual image header and perform the relevant operation (e.g. concatenation) to these data as well; these data would otherwise be very difficult to handle at the command-line interface.

There’s also a documentation page here on diffusion gradient scheme handling if you’re interested (or if you think it lacks certain information that otherwise may have helped, let us know).

5

Thank you as well, yes I’m interested in the diffusion gradient scheme handling. Right now it seems quite clear in the description.