Hi,

I an lesion segmenting some CT scans. After segmenting them in ITK Snap, I normalized them using SPM12 clinical toolbox. The resulting image size is 157 x 189 x 136

However, the atlas size downloaded directly for SPM12 toolbox is not the same size and I cannot overlay.

How can I load atlases so that the sizes match or am I making a mistake during the normalization process?

Thanks!

Thank you so much for your response. I am still a bit confused.

How can I ensure that the atlas I use is the same size as the SPM template? For example, https://www.oxcns.org/aal3.html has the AALvs3 for SPM 12. This atlas has dimensions of 181 x 217 x 181.

How would I set the bounding box to match those dimensions?

Would I manually enter the bounding box as 91 x 109 x 91 to get those dimensions?

There are a couple ways to solve this - you can reslice the scans or the atlas to match the other. If you do reslice the atlas, make sure teh 'interp' is set to zero (nearest neighbor)

https://github.com/rordenlab/spmScripts/blob/master/nii_reslice_target.m

The other option is to set the bounding box for your normalization to match your atlas.\

Do make sure the atlas you use is the same size as the SPM template. SPM templates have an average size, while the MNI templates are larger than average, as seen in Figure 1:

  https://www.ncbi.nlm.nih.gov/pmc/article...

Therefore, you need to make sure your atlas is aligned to the correct space.