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I tried the align_epi_anat.py, but I get this error:
#Script is running (command trimmed):
3dresample -master __tt_T1_skull_removed+tlrc -prefix __tt_IRN-1_Masked_tsh_vr_ts_rs -inset __tt_IRN-1_Masked_tsh_vr_ts+orig'' -rmode Cu
** ERROR: Could not resample
The funny thing is that if I run the 3dsample command by itself, it seems to work just fine.