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Hello FreeSurfers,
In visually reviewing the output of the hippocampal subfield segmentation, there are a few subjects that show gaps in the segmentation. For some, this may be due to variation in intensities in the region, but for others we are unable to tell why this may happen. Some also appear to include more than the hippocampus in the boundaries. Please see the attached examples. This was run with FS version freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Any idea why this may happen? Should we be concerned about the validity of the segmentation, or does it accurately represent the neuroanatomy for these individuals (normal variation vs. pathology)?
Uuummm it’s hard to tell with single slices, but a lot of it is the alveus. There’s also a cyst in one of the cases. King regards, /Eugenio
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Juan Eugenio Iglesias
From: Tricia Merkley tmerkle22@yahoo.com Date: Friday, October 17, 2025 at 18:41 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal segmentation
External Email - Use Caution
Hello FreeSurfers,
In visually reviewing the output of the hippocampal subfield segmentation, there are a few subjects that show gaps in the segmentation. For some, this may be due to variation in intensities in the region, but for others we are unable to tell why this may happen. Some also appear to include more than the hippocampus in the boundaries. Please see the attached examples. This was run with FS version freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Any idea why this may happen? Should we be concerned about the validity of the segmentation, or does it accurately represent the neuroanatomy for these individuals (normal variation vs. pathology)?
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Hi Tricia,
in addition you might check this paper with hints on the QC and normal hippocampal variation.
https://secure-web.cisco.com/1YM1yDiskk1lYTGWYEHcWHUrEUIKwKRLPjtI-sXko1tqgZh...
I would not exclude the case. The alveus is a WM portion of the hippocampus and usually not
forwarded to analyses.
Best,
Philipp
________________________________ Von: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Gesendet: Samstag, 18. Oktober 2025 03:31 An: Freesurfer support list Betreff: [Freesurfer] Re: Hippocampal segmentation
Uuummm it’s hard to tell with single slices, but a lot of it is the alveus. There’s also a cyst in one of the cases. King regards, /Eugenio
--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1RBuDlUPjErgOaaA9Z1rBoJHru7xf6D84BMl_-P7C44JkH4T...
From: Tricia Merkley tmerkle22@yahoo.com Date: Friday, October 17, 2025 at 18:41 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal segmentation
External Email - Use Caution
Hello FreeSurfers,
In visually reviewing the output of the hippocampal subfield segmentation, there are a few subjects that show gaps in the segmentation. For some, this may be due to variation in intensities in the region, but for others we are unable to tell why this may happen. Some also appear to include more than the hippocampus in the boundaries. Please see the attached examples. This was run with FS version freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
Any idea why this may happen? Should we be concerned about the validity of the segmentation, or does it accurately represent the neuroanatomy for these individuals (normal variation vs. pathology)?
freesurfer@nmr.mgh.harvard.edu
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Iglesias Gonzalez, Juan E. -
Saemann, Philipp -
Tricia Merkley