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:
External Email - Use Caution
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.
--
With Regards,
Amar Shukla
PHD Scholar
UPES
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