Hi,
What you describe sounds fine.
Why are you confused after the applywarp command?
This looks like the correct command for getting the probability map into the structural space, assuming that "warped files" is the single warp file that is the output of invwarp.
The output of this applywarp command should be a version of the probability map that overlays directly with your structural image. However, you might find nicer results using trilinear interpolation rather than nearest neighbour, but that is more of a subtlety and should be a cause for confusion.
If you want to then get the probability image into the EPI space then you just need to follow the same steps but with the diffusion to standard warp as the input to invwarp and then replacing the structural with the nodif diffusion image (b=0). This would then resample the probability image into the diffusion space.
I hope this helps.
All the best,
Mark
> On 30 Jun 2017, at 14:13, Yasmine Fathy <[log in to unmask]> wrote:
>
> Hi,
>
> I am new to FSL so I may have naive questions. But I would greatly appreciate your reply.
>
> I am working on an imaging database including T1 and DTI data. For my study, I downloaded probabilistic maps of my region of interest and would like to apply these to the structural T1 images then to DTI.
>
> I did the following:
>
> I used invwarp to calculate non-linear standard to struct. transform.
>
> Then I used applywarp argument: applywarp -i (prob-map) -r (structural image) -w warped files -interp nn
>
> At this point i am very confused.
>
> My general aim is to apply the probabilistic maps to the structural T1 images then convert/transform them to the function image which is the DTI image.
>
> how should I proceed? Do I need to re-do things differently?
>
> Thanks a lot and I look forward to your soonest reply.
>
> Best Regards,
|