Hi Raghav

there are individual steps that can be run, but part of the strength of FreeSurfer is that the comprehensive nature of our modeling gives us greater accuracy. For example, the cortical surface models are used to automatically correct the subcortical segmentation and such. In general compute time is pretty cheap these days, and with a multi-core machine you can cut the run time down to 2-4 hours, so we would recommend just running the whole recon-all pipeline

cheers
Bruce

On Sun, 9 Oct 2016, Raghav Mehta wrote:

Hi,

I am new to freesurfer. I would like to know the command for subcortical segmentation
of brain MRI volume. I read on freesurfer wiki page the recon-all -autorecon2 stage
is useful for this. My question is what exact command should I use for this purpose.
I am familiar with FSL. In FSL 'FIRST' command is useful for this and it gives you
segmentaion in approimately 7-10 minutes. But in freesurfer it is written that
recon-all -autorecon2 stage can take upto 12 hours for segmentation of one volume. I
would like to know if there is any other option for this apart from autorecon2 stage
which can give me segmentation in less time. 

Thank you for your help.

Regards,
Raghav Mehta
MS by Research (ECE)
Center for Visual Information Technology
International Institute of Information Technology - Hyderabad
+91 9712990393

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