1. These need to be image volumes with every voxel containing an index into FreeSurferColorLUT.txt

2. Use the volumes from 1.

3. Yes.

4. The aseg is used to automated several steps in cortical surface reconning that you will need to do manually if you don't have one (ventricle/thalamus/basal ganglia filling, removing brainstem and cerebellum, spackling white matter inferior to hippocampus, etc....)

cheers Bruce

On Tue, 21 Aug 2012, Jeff Thompson wrote:

Hello,  I have a few questions that I hope can be answered:

Q1: How can '.label' files be turned into the necessary '.gca' file needed for the recon-all pipeline. Starting for the first step in auto-recon2. What else other than the '.label' files  would be needed to create this '.gca' file?

Q2:  How to get the seg_edited.mgz file? I would want to use this file in the rebuild_gca_atas.csh script.

Q3: Can the rebuild_gca_atlas.csh script be used to make a replacement for the RB_all_2008-03-26.gca file from the average folder?

Q4: Is there a way to avoid needing the .gca file if cortical thickness measurements is the only goal? Or could there be a limited number of labels needed incorporated into the .gca file for this goal. Ex. Just Cerebral cortex ROI's.

Thank you for any help,

Jeff Thompson