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Great! That's it :) 2017-11-20 17:42 GMT+01:00 Iain D Croall <[log in to unmask]>: > Hi Yasmine, > > If you manage to select the region you want to delete (by getting a binary > "mask" version of it as Rosalina described), you're also then very close to > being able to remove it from the intital atlas. > > If you apply the -binv flag from fslmaths to that binary mask, you'll then > get an "inverted" version of it; i.e. a version of it where every pixel > which isn't part of that region is a "1", and every bit which is is a "0". > > If you then use fslmaths to multiply the original atlas by that "inverted" > mask, the resulting image will be the original atlas but with the region > you extracted removed (all those pixels set to "0"). > > Iain > > On 20 November 2017 at 16:36, Yasmine Fathy <[log in to unmask]> wrote: > >> Hi Rosalia, >> >> You are absolutely correct, the method that Vasudev mentioned is only to >> select a region of interest out of the whole atlas. And I don't want to do >> that, I need to actually remove that region from the atlas so I have an >> atlas minus this region. >> >> I am not sure if selecting the ROI then merging it will then result in >> this region being deleted from the atlas. >> >> I also looked at fslmaths options but can't find anything suitable. >> >> If you find anything out, please let me know :) >> >> Thanks a lot >> >> Best, >> Yasmine >> > >