Hi,

I am having some difficulty transforming a tlrc mask to MNI space. I need to transform a mask generated from EPI data (which is aligned to TT_icbm452 brain) to the MNI152_1mm brain. (Ultimately I need to backproject this mask into each participant's native diffusion space - and the TBSS analysis in FSL is aligned to the MNI152_1mm brain).

I have tried the following
#Transform this mask in tlrc space to MNI space
3dwarp -tta2mni -NN -prefix maskLCerebTonsil_C1_LPG+MNI.nii.gz maskLCerebTonsil_C1_LPG.BIN.nii.gz


However when I look at the newly transformed dataset, the cerebellar region is half-way out of the cerebellum and the post central gyrus region of the mask is almost out of the cortex! (Using my original mask as an overlay on the TT_icbm452 brain, these two points are within the brain).

Then I also tried adding in the newgrid option:

3dwarp -tta2mni -prefix maskLCerebTonsil_C1_LPG+MNI.nii.gz -newgrid 111 maskLCerebTonsil_C1_LPG.BIN.nii.gz

and I also tried with newgrid 333 but made no difference
(but I don't understand this well obviously!)

Any advice would really be appreciated!

All the best,
Jane