Manjari Anant

Hello, yes this is possible. After getting you affine transform 'A' you can run: STalign.transform_points_source_to_target(xv, v, A, pointsI), where xv=None and v=None (because there is no diffeomorphism). 'A' is your...

Hello Leo and Nick, Thanks for using STalign and your detailed description. I believe these issues can be solved by simply padding the images -- I have edited your Jupyter...

Hello, apologies for the delayed response! Which step and what is the error you are encountering?

The scaling factors are related to how the size of the atlas compares to the size of your image. If you plot both of these using plt.imshow() (setting the x...

Hello, Can you please share the image of the slice you are trying to align? Best, Manjari

Hello, It might be helpful if you could also provide an image of what you transform looks like/what regions you are missing as my answer may change. I would not...

Hello, from the diagram it seems like you are not seeing brain regions you expect because there is still misalignment. I would suggest to investigate the intensity values of your...

Hello, yes, thats right! When you find the the tranforms (v and A) using the downsampled image, you can apply these transform on the original image using STalign.transform_image_target_to_source(xv,v,A,[YK,XK], K, [YH,...