We have some resting state images in the SC, C3-C4 levels, kinda non-isotropic resolution (1x1x3).
At the same time, we have saggital T1 and T2, with a large FOV, coregistered with the RS images.
We would like to co-register the RS images to a template and we are having some issues doing so.
We’ve tried various approaches but not a single one of them produces a result good enough.
We have obtained the SC from one of the structural images(T1 or T2) and obtained the warp_anat2template using the whole T1(or T2) image. Applying the warp using sct_apply_transfo to the RS image, not good.
We have also tried to ‘mimic’ the RS FOV to the T1/T2 both image and SC segmentation. Once that has been done, we would follow the procedure of getting the labels, registering the ‘small’ FOV-T1 to the template and trying to apply the obtained warp to the RS image but the results are not what we would expect.
Any ideas on how to proceed?