Hi Sascha,
It sounds like the orientation information is opposite in your mask and your image. If you run "fslorient" on the two images (with no other arguments) you should find that one is reported as being radiological and the other is reported as being neurological. If that is the case then you can swap the mask image orientation by doing the following:
fslorient -swaporient brainmask
fslswapdim brainmask -x y z brainmask
All the best,
Mark
> On 28 Oct 2016, at 16:24, Sascha Frölich <[log in to unmask]> wrote:
>
> Dear all,
>
> I have the following problem:
>
> The orientation of the brainmask I would like to use for data anlysis is different from the orientation of my imaging data. This is to say that, in my imaged data, the voxel which is indexed by the coordinates x,y,z=71,38,50 is projected onto MNI world-coordinates -52,-50,28 (Inferior Parietal Lobule, left hemisphere). However, in the brainmask I am using, the voxel indexed by x,y,z=71,38,50 is projected onto 52,-50,28, which is the same region, but in the right hemisphere. So the projection is basically flipped along the R-L-axis.
>
> Does anyone know how I can transform the brainmask such that the projection is the same as for my imaged data? I hope I explained my problem intelligibly!
>
> Best,
> Sascha
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