Hi,
> Thanks a lot for your reply.
>
> So, for the diffusion to structural, I used epi-reg.
>
> epi_reg --epi=<EPI image> --t1=<T1 image> --t1brain=<skull-stripped T1 image> --out=<output matrix>
That looks good.
> Then I converted the output using convert xfm to get a structural to DTI matrix.
I assumed you just inverted the matrix, which is correct.
> At this point, can I use the applywarp command as follows:
>
> applywarp -i <mask> -o <output image> -r <DTI image> --postmat=<converted mat. file
>
> Is this correct?
This will transform a mask that is in the structural space into the DTI space, yes.
> Or should I use flirt for linear registration?
No need - it is fine to applywarp. Either way is OK.
> Also, since this is seed-based analysis, do I need to register a whole brain atlas to the brains so that it knows where the connections of my region of interest are or not?
If your mask defines your region of interest and it was in the structural space initially then this is fine.
> Another question: What is the best way to analyze this data afterwards? Probabilistic track? I am doing seed-based analysis and would like to apply the same mask to the resting fMRI data I have afterwards. What do you recommend?
That is a very open question. I'm not sure what your hypothesis is and hence what is of most interest. If you want to measure anatomical connectivity then you should use probabilistic tractography. If you want to see whether there are microstructural changes in the WM then we would recommend TBSS. Your resting state analysis can then be seed-based or use dual regression or FSLnets. It depends on what you are interested in and how you want to relate the different measures together.
All the best,
Mark
>
> Thanks again and look forward to your reply.
>
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