External Email - Use Caution
Hi,
I recently attended your FreeSurfer course in June and found it incredibly helpful—thank you! I’m currently working on a research project on AD patients and have been performing quality control on my FreeSurfer outputs using version 8.0.0.
I’d really appreciate your input on a few slices I came across, as I wasn’t sure whether they require manual correction.
In this image, do you think the pial surface (red line) near both hippocampus (light blue) are undersegmented?
[cid:1f744d31-7e4a-40c3-959e-09280cea965e]
This is also another screenshot of the same brain. The pial surface on the left placed inside the WM surface. It's just 1-2 slices but I was wondering what's the best approach to these types of error.
[cid:173d0154-9a5e-49f2-a430-c68849f64d80]
Thank you for your time. Best
External Email - Use Caution
Until the freesurfer gurus can weigh in, I consider this wiki page relevant:
https://secure-web.cisco.com/1fFjmbEDYHyVh2UMcBDoInytFyH3X7Mh2dXtnqxB5BlSgQG...
There are regions where the surfaces are not intended to be accurate that you should be aware of:
Areas around the hippocampus and amygdala. The surfaces will not completely include or exclude certain subcortical regions. These inaccuracies can be ignored as subcortical regions are excluded from the cortical measures and subcortical volume is measured by the aseg, not the surfaces. For an example of this, scroll to coronal slice 128 (slice numbers appear in the upper right hand corner of the viewing window).
From: Mahta Abbaspour mahtaabbaspour96@gmail.com Date: Wednesday, June 25, 2025 at 12:13 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] QC recon- all and manual editing
External Email - Use Caution Hi,
I recently attended your FreeSurfer course in June and found it incredibly helpful—thank you! I’m currently working on a research project on AD patients and have been performing quality control on my FreeSurfer outputs using version 8.0.0.
I’d really appreciate your input on a few slices I came across, as I wasn’t sure whether they require manual correction.
In this image, do you think the pial surface (red line) near both hippocampus (light blue) are undersegmented?
[cid:1f744d31-7e4a-40c3-959e-09280cea965e]
This is also another screenshot of the same brain. The pial surface on the left placed inside the WM surface. It's just 1-2 slices but I was wondering what's the best approach to these types of error.
[cid:173d0154-9a5e-49f2-a430-c68849f64d80]
Thank you for your time. Best
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Yes, Donna is correct. On the 2nd image, it is hard to see what is happening. Make sure to look at other orientations to determine if the surface is placed properly
On 6/25/2025 2:00 PM, Dierker, Donna wrote:
External Email - Use Caution
Until the freesurfer gurus can weigh in, I consider this wiki page relevant:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview https://secure-web.cisco.com/1fFjmbEDYHyVh2UMcBDoInytFyH3X7Mh2dXtnqxB5BlSgQGn_g_ufGIhqCUFZmsou__jI56grxw_uMCdSXzEtaljllEBAC8W_Wf1oZac8ZTHQgJAOyWMMlNx1A0Ltb_TOpRUDfwElZz6h4hyH4F2Wc2QAuBQiwCts8Cwf4-QX1h8p8_2KYI1Uq1tmg8OFpJl6VFzLqulzBMols-MFjr_uhpVhQ4lgKv1wkaOyhdbDdIb7nZIX9n0Y6lFHIccsujag9F9X4mgqQ-1d9_P4suCOflxUQZXKQ608bBsunmocq36x9f3HGiKVI0bmRO_rVf2X/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview
/There are regions where the surfaces are not intended to be accurate that you should be aware of:/
//
/Areas around the hippocampus and amygdala. The surfaces will not completely include or exclude certain subcortical regions. These inaccuracies can be ignored as subcortical regions are excluded from the cortical measures and subcortical volume is measured by the aseg, not the surfaces./
/For an example of this, scroll to coronal slice 128 (slice numbers appear in the upper right hand corner of the viewing window)./
*From: *Mahta Abbaspour mahtaabbaspour96@gmail.com *Date: *Wednesday, June 25, 2025 at 12:13 PM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] QC recon- all and manual editing
* External Email - Use Caution *
Hi,
I recently attended your FreeSurfer course in June and found it incredibly helpful—thank you! I’m currently working on a research project on AD patients and have been performing quality control on my FreeSurfer outputs using version 8.0.0.
I’d really appreciate your input on a few slices I came across, as I wasn’t sure whether they require manual correction.
In this image, do you think the pial surface (red line) near both hippocampus (light blue) are undersegmented?
This is also another screenshot of the same brain. The pial surface on the left placed inside the WM surface. It's just 1-2 slices but I was wondering what's the best approach to these types of error.
Thank you for your time.
Best
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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From: Mahta Abbaspour mahtaabbaspour96@gmail.com Sent: 25 June 2025 18:13 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] QC recon- all and manual editing
External Email - Use Caution Hi,
I recently attended your FreeSurfer course in June and found it incredibly helpful-thank you! I'm currently working on a research project on AD patients and have been performing quality control on my FreeSurfer outputs using version 8.0.0.
I'd really appreciate your input on a few slices I came across, as I wasn't sure whether they require manual correction.
In this image, do you think the pial surface (red line) near both hippocampus (light blue) are undersegmented?
[cid:image009.png@01DBE681.045C2940]
This is also another screenshot of the same brain. The pial surface on the left placed inside the WM surface. It's just 1-2 slices but I was wondering what's the best approach to these types of error.
[cid:image010.png@01DBE681.045C2940]
Thank you for your time. Best
freesurfer@nmr.mgh.harvard.edu
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Dierker, Donna -
Douglas N. Greve -
Mahta Abbaspour -
Roberto Scipioni