Issues with Registration Step in FEAT

[Oumayma]

Hi

I’m running FEAT in FSL. I suspect the issue lies with the registration step,

and I believe adjusting the chosen parameters could help correct it. I’ve attached the parameters I selected. What changes should I make?

Thanks!

[paulmccarthy]

Hi @Oumayma, I would suggest running fslreorient2std and robustfov on both your fMRI and T1 images (and then performing brain extraction on your T1) before running FEAT, to see if that fixes the problem.

edit and also checking the quality of your brain extraction before running FEAT.

[Oumayma]

Hi @paulmccarthy

Thanks a lot for your help. I got this results after reorienting the T1-weighted images,

so I’ll proceed with reorienting the fMRI images as well
and robustfov for both

thanks !

[Oumayma]

Hi again

your point of view plz ! , for 4D fMRI data, when using robustfov, is it possible to process just the first volume, which is often used as a reference for alignment and registration in further preprocessing steps? Or should process all the volumes, given that I have resource constraints?
knowing that I tried splitting the dataset into segments but encountered a problem when attempting to merge them back into a 4D