Dear Pestica-community,

I had a problems regarding the coregistration of my EPI to the MNI-template recently when using PESTICA, version 5. The Pestica tutorial (version 2, pages 22 and 23) states that one should check the coregistration to MNI EPI template while making "sure resp_PESTICA.nii and card_PESTICA.nii line up over your data".

I have worked on two different datasets run within the same patients and MRI run:
1) EPI of wholebrain in low resolution (3*3*3mm) and
2) EPI of reduced FOV covering only the brainstem.

When checking the coregistration of dataset 1) in fsleyes, everything looks fine. However, dataset 2) with the reduced FOV seems not aligned that well, even though my final results look promising. So, I was wondering how Pestica uses card_PESTICA and resp_PESTICA in further processing and whether I could/should change something in the script to fix this (for example adding 3dAllineate as suggested in this post).

Best, Melissa Thalhammer