This is great to hear! The brain mask of the base is created from the cross
runs, and the long runs use the base mask, so you don't need `-synthstrip` for
base or long. I believe it's similar for the aseg but you might have to specify
`-synthseg` when you run the base - not sure, sorry.
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To update my progress, I modified my expert.opts file to only contain a
single line (*synthstrip --no-csf*) and successfully ran recon-all using
the following command:
*recon-all -subjid sub-${sub}_ses-${ses} -i /path/to/anat.nii.gz
-synthstrip -synths
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Hi Malte,
Thanks for this helpful information. Based on your response, I have a few
follow-up questions.
1). Can the expert file (expert.opts) contain a line for the SynthStrip
workflow and another line for the SynthSeg workflow, or do I
need separate
Hi Dan,
I'm afraid these options aren't currently easy to find as they are being parsed
by scripts/rca-config. You can find a set of recon-all options along with a
description in distribution/etc/recon-config.yaml [1].
To pass additional options to SynthStrip, you'll need to specify an expert
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Dear FreeSurfer developers,
I am trying to run longitudinal recon-all -long command. For some subject the
recon-all -long command does not work and the error message indicate that
'transformed geometry does not match". I checked and the initial recon
