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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 >