Hi FSL experts,
I am interested in the functional image in the orbitofrontal cortex (OFC). In my pilot study, each fMRI run consisted of 203 EPI volumes covering the OFC with the following parameters: TR=2 s; TE=22 ms; acceleration factor=3; flip angle=90°; slice thickness= 2 mm, no gap; number of slices=35; interleaved slice acquisition order; matrix size=110 × 110 voxels; field of view=220 × 220 mm. The scanning window was tilted -30° from the AC–PC plane to minimize susceptibility artifacts in the OFC (Deichmann, Gottfried, Hutton, & Turner, 2003). For each subject, 10 EPI volumes covering the entire brain were also collected with the same parameters as described above except 95 slices and a repetition time of 5 s.
After creating the fieldmap, I run the preprocessing using FEAT GUI with following parameters: High pass filter cutoff=100 s. Effective EPI echo spacing=0.253 ms (Echo spacing 0.76 ms divided by the acceleration factor 3). EPI TE=22 ms. Spatial smoothing FWHM = 5 mm.
Registration was performed in a three-step procedure. First, the functional image was registered to the whole-brain EPI (the expanded functional image) (Linear: normal search; 3DOF). Second, the EPI was registered to the T1-weighted anatomical image (Linear: normal search; BBR). Third, the image was registered to the standard brain "MNI152_T1_2mm_brain" (Linear: normal search; 12 DOF). The non-brain structures were removed on these images as recommended.
For the registration to the expanded functional image, I've tried 3DOF and 6DOF. Both registration results do not look good. Especially for the prefrontal cortex in the registration of initial_highres (whole-brain EPI) to highres (T1).
I guess the reason is that the 10 EPI volumes whole-brain images were applied to registration without motion correction, fieldmap correction and averaged.
Therefore, my question is, what are the appropriate steps for registration in this case?
Thank you.
Wan-Yu
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