open-discussion > bug with overlays: left is right
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Oct 3, 2019  09:10 AM | Stefan Katletz
bug with overlays: left is right

I am using MRIcron (64-bit Windows v1.0.20190902) and found two (possibly related) bugs:

1. I am creating an "activation map" from SPECT images with SPM/matlab and save them as nifti. When I load them as overlays on top of an MRI, everything is fine when I use neurological view (left is left). Unfortunately, our neurologists prefer radiological view (left is right), and accordingly the MRI and the overlay are flipped. However, the crosshair will then give me some "random" values from the other side of the brain, which can be quite confusing (and leads to unnecessary discussions when I click on some bright blob and the numerical value is real low...)

2. I also use "labels_Neuromorphometrics.nii" which comes with SPM and unwrap it to the patient's MRI. Then I change the header ( to use it as an anatomical overlay/labels. Again, left and right labels are swapped (probably since the lookup values are obtained from "the other side"). I can make the labels seemingly correct (by invoking the Flip L/R), but the background image is also flipped (of course), adding further to the confusion.

Another thing that I noticed is: after unwrapping the labelmap (from MNI space to the patient's head) the match is nearly perfect. However, by changing the header ("Regular" value to 98 and Statistics->Labels, leaving all other values untouched), the nifti image is slightly shifted, i.e. the overlay does not match the MRI perfectly. One can see the shift by loading the unwrapped nifti files before and after changing the header.

Any suggestions?
Sep 8, 2020  12:09 PM | Chris Rorden
RE: bug with overlays: left is right
Resolved in upcoming release. Users should ensure that the SForm is not modified when changing the intention field.