I am trying to align an anatomical image (anat.nii) to an epi (bold_e2.nii) and would like the procedure to also:
- motion correct all epi’s to volume 5
- skull strip all epis
I have been using:
align_epi_anat.py -anat anat.nii -child_anat roiMask.nii -epi bold_e2.nii -epi_base 5 -save_Al_in -save_vr -save_epi_ns
This appears to correctly align my anatomical to the base epi image, but the skull stripping is only applied to the base epi (as output to bold_e2_epi_in_3dAl_al+orig.BRIK). However, I would like all of the epis to be skull stripped, not just the base.
Thanks in advance.