sorry, nothing attached
On 7/15/2024 4:04 AM, Tornabene, Danilo wrote:
External Email - Use Caution
Hi, and thank you for your answer.
Subject 001 does, indeed, have a misalignment as well, and I don't
know why ( I checked the files are from the same subject - I can't
give you a freeview command as I'm using a different software to view
the results). Subject 017 (also attached) as well as most/all others,
however, have good alignment but very poor segmentation.
I attached the misaligned picture as well because I thought it could
give some hint on the problem that occurred.
Best,
Danilo
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Sunday, July 14, 2024 4:56:22 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Very large segmentation errors with recon-all
what you are showing there is not a segmentation error but a severe
misalignment. What is your freeview command line? Are you sure that
the anatomicals and the surfaces are from the same subject?
On 7/10/2024 4:59 AM, Tornabene, Danilo wrote:
External Email - Use Caution
Dear FreeSurfer developers,
I've encountered very large, systematic errors in segmentation
running recon-all on a MRI dataset of 76 subjects. In the screenshot
attached, you can see how the white surface (shown in the right
hemisphere) includes most of the cortex as well, while the pial
surface (in the left hemisphere) extends into the CSF and often
reaches the skull. In some of the subjects there is also a clear
misalignment with the T1 images.
I don't have a long experience with FreeSurfer, but my supervisor
Prof. Cole tells me he has processed thousands of scans and never
seen this kind of errors so we thought of reaching out to you for
some help or explanation. The only thing we noticed is that this
error happens on scans with a higher-than-usual resolution (voxels
are 0.8x0.8x0.8 mm), could this be causing the problem?
I have simply ran recon-all withouth any additional option or
argument other than the input files and IDs and the output directory.
Please find the shell log outputs for two sample subjects. The
recon-all pipeline was completed with no hard errors, and the Euler
numbers were mostly 2 with some 1.
Best,
Danilo Tornabene
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