Hi Bruce,
Thanks for your help. Is it possible if I do the surface-based segmentation alone. If so, then what are the commands I would be using? I appreciate your help.
Shahab
Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Shahabuddin,
if you just do:
recon-all -i [input] -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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