Nurunisa,
Yes, you can add just -gca GCA_ALL to the command line, but you will need to also need to add -no-wsgcatlas to recon-all, because the skull- stripping step uses the gca_withskull atlas.
For added measure, if you only want to use your own atlas, you might want to move or rename the RB_all_*.gca files, to ensure that you dont accidentally mix usage with your own atlases.
Nick
On Mon, 2008-12-01 at 10:59 -0500, Nurunisa Neyzi wrote:
Hi,
if I want to use an alternative subcortical atlas (and I only have the equivalent of GCA_ALL but not GCA_SKULL), can I just add -gca GCA_ALL to the command line? Is there anything else I need to do?
thanks,
Nurunisa
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