External Email - Use Caution
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 Pipelines, not run by itself for optimal performance in HCP data.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of yunus soleymani
<soleymani.yu...@yahoo.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, December 4, 2023 at 7:53 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] skull stripping error
External Email - Use Caution
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 thicknesses. The advice is always to use the latest
version. We plan to perform the volumetrics using version 7.4.1 of Freesurfer.
Then, we will use both our results and the original HCP runs in our modeling,
and maybe compare them.
bests,
Yunus
On Monday, December 4, 2023 at 05:00:40 PM GMT+3:30, Glasser, Matt
<glass...@wustl.edu> wrote:
External Email - Use Caution
Why are you rerunning FreeSurfer on HCP data? You are unlikely to match the
quality of the original FreeSurfer runs.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of yunus soleymani
<soleymani.yu...@yahoo.com>
Reply-To: Freesurfer Support List <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, December 4, 2023 at 4:59 AM
To: Freesurfer Support List <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] skull stripping error
External Email - Use Caution
Hello Freesurfers,
I recently analyzed about 600 subjects from HCP database using the Freesurfer
recon-all algorithm. However, I noticed that in almost one third of the
subjects, the software did not perform the skull stripping correctly when I
checked the results in Freeview. To address this issue, I repeated the skull
stripping step for each subject using the code "recon-all -skullstrip -wsthresh
35 -clean-bm -s <subject name>". The skull stripping went well, and then I
repeated the analysis using the code "recon-all -autorecon-pial -subjid
<subject name>".
When I compared the pre and post-correction stats folder, I noticed that some
volumetric values had changed, especially in the specific areas related to the
initial skull stripping error. However, my concern is that when I loaded the
.pial and .aseg files into Freeview, there was no change compared to before the
correction visually. Is this okay, or should I take additional steps? I would
appreciate your help.
Thank you,
Yunus
Bellow is an example. NumberS 1 and 2 are brain masks before and after
correction. Numbers 2 and 3 are superimposed .aseg files before and after
correction.
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