I found the option here <http://surfer.nmr.mgh.harvard.edu/docs/recon-all.help.txt> 

And out of curiosity, I ran autorecon 1 followed by -subcort-seg then mri_segstats and see how large the difference is and using the faster computational approach most of the subcortical ROI volumes were slightly underestimated. We have about 500 T1s is the reason for using the faster computational approach, it is evident there are going to be differences...for the time being we will most like try to run recon-all with the surfaces and using as many different options to speed it up.

Thanks for the help!


On Sun, May 1, 2016 at 11:46 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
what is -nosphere? I don't think it'sa  recon-all option, is it?

I guess I would recommend running things all the way through unless you really don't have the compute time/disk space

cheers
Bruce




On Sun, 1 May 2016, Taha Abdullah wrote:

Hello Burce,
Thank you for the reply, I see well I would want to use the surfaces then.
Would you recommend something like running recon-all and using -nosphere?

-Taha

On Sat, Apr 30, 2016 at 1:14 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      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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--
Taha Abdullah 
Department of Physiology
Northwestern University 
Masters of Science Physiology and Biophysics, Georgetown University 2015


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




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