Hi everyone,
I hope this message finds you well. I’m relatively new to FSL and am currently working on preprocessing fMRI data for a project. I’m encountering some challenges with the registration, which isn’t quite aligning as expected.
I have experimented with a few parameters such as degrees of freedom (DOF), search space adjustments for registration to the main structural image, and adding a cost function, but unfortunately, these changes haven’t improved the registration.
I’ve attached an image showing the current results of the registration. I would greatly appreciate any guidance or suggestions you might have to help improve this process.
Thank you very much for your assistance!
Best regards,
Mary
I would recommend using the FSL jiscmail forum for questions specific about FSL.
- The EPI scan has little signal from the scalp, while the scalp is prominent on the T1 anatomical scan. I would suggest using FSL’s BET on each first (with perhaps -f 0.3 for the EPI and the default -f 0.5 for the anatomical) and running FLIRT on the EPI based scan.
- The EPI scan has T2-weighted contrast (CSF bright, fat gray), and the anatomical scan has T1-weighted contrast (CSF dark, fat bright). Therefore, void intra-modal cost functions. I would suggest
-cost mutualinfo.
- Given that the anatomical scan does not have the geometric distortion of the EPI, you will certainly want to use
-dof 12. As I recall, the FEAT interface will default to dof 9 if one of the scans has a field of view less than 120mm in any dimension. Therefore, when acquiring EPI scans, it is important to make sure that you have at least 120mm in the slice direction.
You might also want to check out the FSL course online materials
I will check these out. Thank you so much!
