Dear Marco,
You need to use "invwarp" to get the inverse of the FNIRT warp.
It is best if you use FNIRT to do the registration form your image _to_ the MNI image, and after this invert the warp.
Hope this helps.
All the best,
Mark
On 24 Sep 2012, at 11:19, Marco RC <[log in to unmask]> wrote:
> Dear FSL experts,
>
> This is my first time writing to this mailing list and I am very happy for having the opportunity to get some support from FSL advanced users. I just got started with FSL and the tutorial is being very helpful.
>
> I am aiming to calculate grey and white matter in a stroke patients population with severe and huge lesions. I saw some different approaches to perform such analysis, but I am trying to stick to a published one performed in a very similar stroke population I am having access to. What I've been trying to do (without much success up to now) is:
> 1) Bet skull extraction
> 2) Tissue segmentation with FAST (3 classes - pves)
> 3) Transformation to MNI space with FNIRT
> 4) To use of MNI-space ventricular mask to remove in FAST-pves any part of the lesion that included portions of the ventricles
> 5) Transformation of pves mask to the original subject space using the inverse non-linear warp field
> 6) To use pves mask for subsequent non-linear registration iterations (10x)
> 7) Visual inspection and manual corrections (if necessary)
> 8) Tissue loss in GM and WM calculus
>
> However, different from other people who normally deals with stroke brain tissue segmentation, I have only T1 images available. My questions are:
> 1) Does anyone have a more optimal protocol to suggest or strong critics about this one?
> 2) After performing steps 1 to 3 I think I did the step 4 successfully by typing in the terminal:
>
> $FILEDIR/standard/MNI152_T1_2mm_VentricleMask -sub STR_241_pve_0 STR_241Vent_pve_0
>
> Then I got stuck in the next step (step 5), as when I performed FNIRT I could use the following command as "reference" to base mine:
>
> fnirt --in=old_subj --aff=flirted_old_brain.mat \
> --config=T1_2_MNI152_2mm.cnf --cout=coef_old_subj_to_MNI152 \
> --iout=fnirted_old_subj --jout=jac_old_subj_to_MNI152 \
> --jacrange=0.1,10
>
> because I was transforming to MNI space, but now I dont have a .cnf to use from my original subject file to make this transformation back. Any suggestions? By the way, is FNIRT mandatory prior to do this inverse non-linear warp field?
>
> Greetings to all and thanks in advance for your time and attention,
> MRC
>
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