There are 100s if not more parameters in recon-all supporting dozens of underlying functions. If you look in recon-all.cmd (or .log) you will find the binaries that get called; sometimes the command line has parameters, sometimes the parameters are embedded in the binary itself. Some of the defaults are in the recon-all script or the recon-config.yaml file. There is not really one paper that describes everything as many of the functions have evolved over the years, many with their own papers.

On 5/31/2022 8:07 AM, Amar Shukla wrote:

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Dear Sir,

I am a PhD scholar using the freesurfer tool to conduct my research work. I tested the recon all method in the Free Surfer, and it was effective with the data set that was used by me. What are the exact default parameters for the different processes of recon all that were used in motion correction, intensity normalization, etc?. It would be really helpful if you could provide me with the link or the article where it is explained clearly, this will help me to get through these processes in more depth and in a more constructive manner. Although the Free Surfer website has an FAQ regarding this process, there are no clear explanations about what the default parameters are during recon all.

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With Regards,

Amar Shukla

PHD Scholar

UPES
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