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Why are you rerunning FreeSurfer on HCP data? You are unlikely to match the
quality of the original FreeSurfer runs.
Matt.
From: on behalf of yunus soleymani
Reply-To: Freesurfer Support List
Date: Monday, December 4, 2023 at 4:59 AM
To: Freesur
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Yes, you are right. However, the original HCP runs were based on Freesurfer
version 5.3, which is an older version. Recent studies have reported
significant differences in Freesurfer outputs across versions, especially in
the case of cortical thickne
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FreeSurfer 7.X is not working well with HCP data right now, so your results
will be substantially less accurate (this is being actively worked on by the
HCP group and FreeSurfer group). Also, FreeSurfer needs to be called as a part
of the HCP Pipeli
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Alright, we were not aware of this point. Thank you very much for informing
us. However, we would like to know your suggestion regarding rsfMRI data. Is it
advisable to work on unprocessed data using the currently available software,
or should we do
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I would just use the preprocessed HCP data and not try to redo any of it.
Matt.
From: on behalf of yunus soleymani
Reply-To: Freesurfer support list
Date: Monday, December 4, 2023 at 8:12 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] s
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Hello,
I am trying to generate the surfaces ‘brain.surf’, ‘inner_skull.surf’,
‘outer_skull.surf’ and ‘outer_skin.surf’. When I use ‘mne watershed bem’, I
obtain surfaces that are in the wrong order (eg. brain.surf is outside of
the inner_skull.surf’)
Hi,
‘mri_binarize –replace v1 v2’ performs transitive replacements if multiple
‘–replace’ args are specified. This has been the behavior since May 25, 2021
commit.
Now, new mri_binarize option '--no-transitive-replace' is introduced to turn
off the transitive replacements. Let me know if this
