Hello everyone,
I trying to align dwi data to the MNI atlas however I am facing some issues. I have read the previous posts about aligning dwi data to t1 and used the suggested codes -but even though the alignment improved, it did not completely fix the issue. I would also like to point out that it worked in some patients with tumor subjects but did not work properly in some patient with tumor subjects.
The code I am using now is the following-----Number 1 for sick subjects
And the atlas alignment is like this:
*** I also want to add that I used another code for healthy subjects which made a proper alignment but did not work in sick subjects. It was the following code,I changed this Number 2 code to the Number 1 code so that I can align MNI atlas to dwi in sick subjects as well.
Number 2 Code
When I use this code I get the proper alignment in healthy subjects like this:
My main problem is that by using Number 1 code I cannot get the proper alignment in SOME OF the sick subjects even though it works mostly good in other sick subjects.(Note:code Number 2 also worked for some sick subjects as well.But failed the MOST of the sick subjects)
Does anyone know how to fix this issue, it would be of great help.