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Hi Eugenio,

Happy to share that with you. I am pretty new to Freesurfer, so could you clarify what volumes you would like me to share? I currently have "aseg.mgz", "rh.hippoAmygLabels-T1.v21.FS60.mgz", "lh.hippoAmygLabels-T1.v21.FS60.mgz", and "nu.mgz" loaded in my 2d screenshots I sent. Also, would you like me to send these using the FTP file exchange? 

Thank you!


Angel Hammond

Research Specialist

Center for Healthy Minds

University of Wisconsin-Madison



From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Sent: Monday, August 10, 2020 9:14 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Medial Nucleus Errors
 

Dear Angel,

It’s hard to tell without seeing the segmentation in 3D. Would you mind sharing, please?

Cheers,

/Eugenio

 

 

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com 

 

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Angel Hammond <ahammond3@wisc.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, August 10, 2020 at 10:11
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Medial Nucleus Errors

 

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Hello Freesurfer Experts,

 

I wanted to re-post a portion of a question that a previous team member posted on June 20th, 2019 (See: Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors)

 

We have visually checked 116 subjects that have been processed using

Freesurfer's latest hippocampal/amygdala subfield segmentation

and came across a few cases that had questionable segmentation. The T1s had were processed using

FS 5.3, and we used the command "segmentHA_T1.sh" from the latest Dev

version.

 

-We have come across about 5 subjects' medical nuclei masks that are located in the Putamen region (more superior/detached from the rest of the amygdala) on one side of the brain (in some cases just the right side, in other cases just the left side). In all of the other subjects, we don't see that same detached looking segmentation into the putamen on one side as these few show. I will attach screenshots to show this. 

 

-I have checked the aseg for these subjects as suggested in the previous question, and the hippocampus, amygdala, and putamen all look fine there. I have also checked the output volumes for the medial nucleus of these subjects and the numbers all look fine. 

 

-So, my main question is:  If the placement of the medial nucleus is wrong in the segmentation (detached/in the putamen as shown) but the aseg looks correct, can we still use those values reliably? 

 

Thank you!

 

 

Angel Hammond

Research Specialist

Center for Healthy Minds

University of Wisconsin-Madison