Hi
If you have a mask in MNI space that you want to transform into DTI space, you can proceed as follows:
- Compute (1) DTI->Struct and (2) Struct->MNI transformations
It is best if (2) is nonlinear (e.g. with FNIRT).
(1) can be linear (FLIRT) provided you have corrected the DTI for nonlinear distortions (fieldmap or topup)
- Invert the transformations (1) and (2) with invwarp
- Concatenate the two transformations to get DTI->MNI and MNI->DTI (with convertwarp)
- Apply the transformation MNI->DTI to your mask with applywarp.
Cheers
Saad
> On 3 Jul 2017, at 09:31, 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 functional 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,
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