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Hi Vasilis You don’t have to transform your masks. You can provide the masks in MNI space and then give probtrackX the transforms from diffusion to MNI space. The rest will be taken care by probtrackX. See example on seeding from MNI space here: http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt2/index.html#tractography Cheers Stam On 6 May 2015, at 13:22, Vasilis M. Karlaftis <[log in to unmask]> wrote: > Dear FSL users, > > I was trying to find out what is the best way to create a mid sagittal mask to use it as an exclusion mask in ProbtrackX. I didn't find any details on how to create it, so here I am. > > 1) My first attempt was to define a mask in MNI space. I opened MNI152_T1_1mm_brain in fslview and for X=90 I created a mask with the fill tool in sagittal view. This created the mid_sagittal_mask file. > > The problem with this approach is that when I tried to align this mask to each subject's native space, it resulted in some gaps due to rotation (?). These gaps resulted in "failure" of the exclusion of interhemispheric connections. You can see the result in mid_sagittal_mask_aligned. > > I used a linear alignment of the mask as follows: > flirt -in mid_sagittal_mask -ref data_ecc -applyxfm -init FA_to_native.mat -interp nearestneighbour -o mid_sagittal_mask_aligned > > > 2) I tried a mid sagittal mask twice as thick (X=90 & X=91) but the outcome was similar. Thus, I decided to go on with a half hemisphere mask (see left_hemisphere_mask). The alignment of this mask to each subject's native space was good. > > I am not sure though if this is acceptable to run tractography with such a big exclusion mask for this purpose. > Looking forward to your advice. > > > Thanks for your help, > Vasilis > <mid_sagittal_mask.JPG><mid_sagittal_mask_aligned.JPG><left_hemisphere_mask.JPG><left_hemisphere_mask_aligned.JPG>