Notes about the following pipeline document
The "registration to standard space" of the T2 structural image is not performed automatically by TORTOISE. Instead, it is something we recommend users of TORTOISE do outside of our software, as the desired standard space may be different depending on the user's specific dataset.
Recommendations and Requirements for standard space registration of T2 structural images:
- The T2 structural image must remain anatomically faithful - meaning no affine or non-linear warping steps should be performed. This is vital for proper performance of the EPI distortion correction step, which uses image registration to match a non diffusion weighted (b0) image to this T2 structural image to correct for EPI distortions.
- We recommend putting your T2 image into an ACPC alignment, including a midsagital alignment. This assures consistency between datasets, aligns the data so that the color encoding looks as expected, and also provides a good initial consistent orientation from which to perform further processing steps, such as tensor based registration. Many software packages have an ACPC alignment option. We generally use mipav.