Hey,
Is 3dAutomask (generally) more generous in it’s estimation of the brain when skullstripping EPI images than 3dSkullStrip?
I ask because in this screen shot https://www.dropbox.com/s/rk48mboy3eb1v9f/screenie.png?dl=0 (run on the same data from the same subject), on the left can be seen an invocation of align_epi_anat.py with 3dSkullStrip as the default and on the right is an invocation of aea with 3dAutomask as the skull stripper. Both invocations produce good alignments but the extent of the brain from the invocation involving 3dAutomask is clearly bigger.
Is there a reason to prefer 3dAutomask over 3dSkullStrip fro skullstripping EPI data?
LEFT AFNI:
align_epi_anat.py -anat2epi \
-anat ${anatFile} \
-epi ${epiFile} \
-epi_base 0 \
-volreg off \
-tshift off \
-cost lpc \
-multi_cost lpa lpc+ZZ mi
RIGHT AFNI:
align_epi_anat.py -anat2epi -anat bc002b.anat_unif+orig \
-suffix _al_keep \
-epi vr_base+orig -epi_base 0 \
-epi_strip 3dAutomask \
-cost lpc \
-volreg off -tshift off