Hi Lucas,

I guess I would modify recon-all to change the nu_correct line to a cp.

cheers, Bruce On Thu, 26 Feb 2009, Lucas Eggert wrote:

Dear Experts,

I would like to compare different processing procedures for the classification of gray matter. For this purpose, I would like to compare e.g. FreeSurfers default processing stream for subcortical labeling with the result that you get, if you leave out bias correction (nu_correct) in this processing pipeline, or replace N3 with another bias-correction algorithm. But, it appears to me, that the subsequent steps always look for the output-file of the previous processing step that would have took place in the default processing.

So, my question is: How can I most efficiently leave out or replace single processing steps in FreeSurfer's default processing stream?

Any help would be very much appreciated.

All the best, -Lucas _______________________________________________________________________ DSL zum Nulltarif + 20 Euro Extraprämie bei Online-Bestellung über die DSL Freundschaftswerbung! http://dsl.web.de/?ac=OM.AD.AD008K15279B7069a

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