Hi Shahabuddin,

if you just do:

recon-all -i -all

it will do everything (subcortical and cortical)

Bruce
On Tue, 12 Sep 2006,
Shahabuddin Ansari
wrote:

> Hi,
>
> I have done volume-based segmentation using freesurfer
> and now am interested in surface-based segmentation. I
> have used the following set of commands in
> volume-based segmentation:
>
> #!/bin/csh
> # Shahab Ansari, August 22, 2006
>
> #The following command creates a directory structure
> for the subject, and strip skull, normalize intesity
> and normalize coordinates
>
> recon-all -i /ensc/IMAGE/2998977_02/2998977_02.img -s
> 2998977_02 > 2998977_02.log
>
> recon-all -subjid 2998977_02 -autorecon1 >>
> 2998977_02.log
>
> #this command segments the subcortical brain and takes
> about 10 hrs
>
> recon-all -subcortseg -s 2998977_02 >> 2998977_02.log
>
> #this will translate the segmentation back to the
> original MRI space
>
> mri_convert -rl
> /ensc/IMAGE/opt/FREESURFER/subjects/2998977_02/mri/rawavg.mgz
> -rt nearest
> /ensc/IMAGE/opt/FREESURFER/subjects/2998977_02/mri/aseg.mgz
> /ensc/IMAGE/opt/FREESURFER/subjects/2998977_02/mri/aseg_raw.mgz
>>> 2998977_02.log
>
> I need some know what else I need to do to segment the
> cortical surface. I appreciate any help pointer.
>
> Thanks
> Shahab
>
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