Hi Taha

you can, but it won't be as accurate since the surfaces give better estimates of cortex and such (and we use them to automatically correct the aseg). You can run the individual steps through the end of mri_ca_label if you want to stop there

cheers
Bruce

On Fri, 29 Apr 2016, Taha Abdullah wrote:

Hello All,
I am running an analysis strictly on subcortical volumes, and to save time
and disk space I wanted to avoid if possible construction of surfaces and
seems that it is necessary? I first ran recon-all -autorecon1, second I ran
recon-all  -subcortseg and the final error was regarding no such file or
dir, specifically the  /surf/lh.white.

Is there a better way to run this type of analysis to save disk space and
time? Possibly using -autorecon2'; would love any input. Thank you in
advance!

--
Taha Abdullah 
Department of Physiology
Northwestern University 
Masters of Science Physiology and Biophysics, Georgetown University 2015

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