open-discussion > Overlay misaligned
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Feb 27, 2019  02:02 PM | Emily Dennis
Overlay misaligned
I'm trying to make some figures but running into an odd and hopefully basic issue. I open my anatomical image then try to add the statistics as an overlay but it appears to be centered differently. Viewing these files in other programs I don't have this issue, so I know they are in the same space. Any thoughts on what might be causing this?
Attachment: overlay.png
Feb 28, 2019  10:02 AM | Emily Dennis
RE: Overlay misaligned
It appears this misalignment is an issue in the 2018 version. In the 2016 version I'm having a different issue - the overlay appears to be aligned, but it won't show the range of values in the image. I'm trying to overlay a map of T-stats that I know range between -6 and 6, but I'm getting 1 color. 
Help with either of these issues would be great - misalignment but proper values in 2018, proper alignment but not showing range of values in 2016.
Attachment: Tval.png
Mar 1, 2019  06:03 AM | Chris Rorden
RE: Overlay misaligned
1. Can you provide the NIfTI image you are using as your overlay?
2. Can you describe what "other programs" you are using?

I think if you use SPM's Check Reg to look at this overlay, you will see that it is not aligned to the background image. I think the "other programs" you are using are ignoring the NIfTI S-form. Seeing the images will test this hypothesis.

The one challenge with NIfTI is that it has two spatial transforms (the S-Form and the Q-Form). In situations where they both exist and where they conflict different tools behavior differently. SPM, FSLEyes, MRIcroGL, etc give precedence to the S-Form (which makes sense, as it has more degrees of freedom so is better for handling registrations). On the other hand, ITK based tools (Slicer, ANTS, etc) give precedence to the Q-Form. This means that images that appear aligned with SPM may have a poor starting estimate for ANTS. For this reason, if you have multiple tools, it is worth setting these to the same spatial transform (recognizing that the Q-Form can not store shear transforms).
Mar 4, 2019  02:03 PM | Emily Dennis
RE: Overlay misaligned
Ah thank you that was it! I had been viewing it in FSL, I just had to copy the qform/sform info to my stats image, now it works.

Thank you!