Hello Dr. Ashburner,
Thank you for the response. Do you have any thoughts or suggestions for how to improve the results?
I attached the script that produced those results (it is also located at: http://jamiehanson.org/SPM_list/spm_restALL_new.m). The basic steps were:
1) Slice time correct EPIs (based on our interleaved acquisition, default params)
2) Realign and unwarp STC’ed EPIs (default params)
3) Segment the T1 with new segment, native space + dartel import for GM & WM, native space for the rest
4) generate skull stripped T1 based on seg. output (GM + WM + CSF)
5) coregister (dont reslice) meanu*img (from EPI realign/unwarp step) to skullstripped T1, along with all the R&U’ed EPIs
6) create DARTEL warp for DARTEL imported GM & WM to VBM ISI550_MNI152 templates (using all 6)
7) Used DARTEL MNI normalization with flowfields from step 6, with the coreg’ed EPIs from step 5 as additional images
EPIs are collected at 3.75x3.75x4mm voxel size. T1 coplanar has 0.9x0.9x4mm voxels
Any ideas are greatly appreciated!