Douglas, Let's try with an example. See the two ways<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all> 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<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> 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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