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Neural-Systems-at-UIO / QuickNII

https://quicknii.readthedocs.io
MIT License
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Bregma values as listed in quicknii inaccurate #19

Open ingrre opened 2 years ago

ingrre commented 2 years ago

Hello,

I wanted to extract the bregma value for the WHS position of my registration and noticed it did not match well. Checking further, I believe the following registration of the Paxinos atlas (2007) to the WHS template should make a fairly good match between the bregma listed on each section plate and the reported value in QuickNII. It does not (of course relative depending on the level of accuracy desired). Get xml file here: Z:\ReferenceAtlas_Anchoring\Rat\RBSC_Paxinos-Watson\Edition6_2007\coronal\diagrams (Z is lagringshotell.uio.no)

I would be interested to hear if this is supposed to be only an approximate value or if it would be possible to improve this.

Tevemadar commented 2 years ago

The transformations present in QuickNII use raw NIfTI directions, so it's just an approximation now. WHS SD Rat template has a 4-degree deviation from flat-skull orientation, and it matters (that's why all the PW plate anchorings have a 4-degree angle in the sagittal plane). I will provide a rotated transformation to test, but not today.

Majpuc commented 1 year ago

This still need to be adressed @Tevemadar Does this require a change in QuickNII?

Majpuc commented 9 months ago

Todo list for new WHS release in 2024: