Douglas,

Let's try with an example. See the two ways T2 image can be integrated with recon-all

Altogether:

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all

autorecon3 only:

recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3

Similar to the former, -hippocampal-subfields-T1 integrated with recon-all:

recon-all -all -s bert -hippocampal-subfields-T1

Now the question, compared to the latter, which autorecon[1/2/3] would accept -hippocampal-subfields-T1?

Does it make sense now?

-Tashrif

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