Hello again,
Following a reply i got, I'm adding some information that might help you help me:
Since including a segmentation phase distorted our images, we've omitted it and our pre-processing looks as follows:
1. Realign & Unwarp
2. Slice timing
3. Co-registration: Estimate (reference: mean unwarped EPI image. source: our anatomical image)
4. Normalize: Estimate & Write (source: co-registered images. images to write: EPI images. template: SPM8 T1 template image)
5. Smoothing
Does this look ok to you? (we've also tried to skip the co-registration and normalize the EPI images according to SPM8 EPI template images, but we got similar results).
Thanks,
Asaf.
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