Dear Mike,
Please check the following:
1) Did you cover the "missing" parts of the brain with your EPI sequence? Subjects might have moved out of the field of view during the session.
2) Did coregistration between mean EPI and anatomical T1 volume work well (in case you used that step)? If not, then usually you can improve the results of coreg by reorienting the EPI data to better match the orientation of the T1 before (or vice versa, or possibly reorient both the EPI series & mean to AC-PC in one step and the anatomical T1 in another step).
3) Did segmentation/normalisation work well (compare the w* files and template images / tissue probability maps in SPM)? If not, then usually this is due to very different alignment of the acquired data compared to the templates, again, reorientation before should help.
In your case, also check whether there are any extreme susceptibility artefacts in that particular subject. If this doesn't solve your issues feel free to provide some links to the raw T1 and EPI mean and the normalised versions.
Best
Helmut
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