BUG: Images are not aligned in FSLeyes

[pauldmccarthy]

Checklist

• I have checked that this issue or question has not already been reported on this issue tracker
• FSL version: 6.0.4 (tip: run cat $FSLDIR/etc/fslversion in a terminal)

• Operating system: Ubuntu 18.04 (tip: run uname -a in a terminal)

Describe the problem

Hi, I am trying to look at two images in FSLeyes, but they appear on different parts of the screen. They are from the same subject, so should be aligned, but appear like this instead:

I've attached the images to this issue. Any help would be appreciated!

MNI152_T1_2mm_brain_mask.nii.gz

MNI152_T1_2mm.nii.gz

Also, sometimes when I start up FSLeyes, all of the icons look like bums. What's with that?

[pauldmccarthy]

Hi, this mis-alignment can happen when the voxel-to-world transformation of one of the images has been changed somehow. For example, if you created and saved your mask image in a MATLAB session, the transformation may not have been saved correctly.

If you are 100% sure that the images are voxel-aligned (i.e. the same voxel corresponds to the same anatomical location in both images), you can use the fslcpgeom command to copy the transformation information from one image to the other. For example:

fslcpgeom MNI152_T1_2mm MNI152_T1_2mm_brain_mask

I'm not sure about your other issue, sorry.