Dear Saurabh, Is this recon-all (aseg.mgz), or the hippocampal subfield module? 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 "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:30 To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hipppocampal segmentation on freesurfer
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External Email - Use Caution Hi experts,
I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass?
Saurabh
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Hi Eugenio,
This is recon-all (aseg.mgz), and not the subfields. Thanks
Saurabh ________________________________ 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: Tuesday, April 20, 2021 10:36 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
* External Email - Caution *
Dear Saurabh,
Is this recon-all (aseg.mgz), or the hippocampal subfield module?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1C0u8xLvDh4rlmpEJA1NgIB9ww1gy1q7aBCCorYzXS_bga3E...
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:30 To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hipppocampal segmentation on freesurfer
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Hi experts,
I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass?
Saurabh
________________________________
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.
________________________________ 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.
If you’re only/mostly interested in the hippocampus, I’d encourage you to try the subfield module 😉
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 "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:39 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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External Email - Use Caution Hi Eugenio,
This is recon-all (aseg.mgz), and not the subfields. Thanks
Saurabh ________________________________ 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: Tuesday, April 20, 2021 10:36 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
* External Email - Caution *
Dear Saurabh,
Is this recon-all (aseg.mgz), or the hippocampal subfield module?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1C0u8xLvDh4rlmpEJA1NgIB9ww1gy1q7aBCCorYzXS_bga3ESZfuxRTmq_f61IYiq-4CVUbbG9oarENS_seMmdRQzwHJ9rCx6Y26tbt-SnIp4cfPTggOGOv88bgGwBuJF0uLYoZOMD5xNNRMSmUYp7FHyA7XvHGsAEcVCM7njP9AlzsrK1YGQd0Imc6rz17ipZbkOe5TEK8BaiyLe02Jnrv7l-onBsLBb4plIgxQES6oncBpR9aQLbfRMzlTOo5BkgPo4GLf9OujZ2JZBDLe8lA/http%3A%2F%2Fwww.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:30 To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hipppocampal segmentation on freesurfer
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Hi experts,
I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass?
Saurabh
________________________________
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.
________________________________ 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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Okay, so could I expect better segmentation results from that without having adjacent choroid plexus/white matter included as hippocampus.
Saurabh ________________________________ 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: Tuesday, April 20, 2021 11:06 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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If you’re only/mostly interested in the hippocampus, I’d encourage you to try the subfield module ??
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1jbrnfE7ASTieSRrFULjRTTLKXWnwHAhue72Z4nJzPdABrM7...
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:39 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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External Email - Use Caution
Hi Eugenio,
This is recon-all (aseg.mgz), and not the subfields. Thanks
Saurabh
________________________________
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: Tuesday, April 20, 2021 10:36 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
* External Email - Caution *
Dear Saurabh,
Is this recon-all (aseg.mgz), or the hippocampal subfield module?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1jbrnfE7ASTieSRrFULjRTTLKXWnwHAhue72Z4nJzPdABrM7...http://secure-web.cisco.com/1C0u8xLvDh4rlmpEJA1NgIB9ww1gy1q7aBCCorYzXS_bga3ESZfuxRTmq_f61IYiq-4CVUbbG9oarENS_seMmdRQzwHJ9rCx6Y26tbt-SnIp4cfPTggOGOv88bgGwBuJF0uLYoZOMD5xNNRMSmUYp7FHyA7XvHGsAEcVCM7njP9AlzsrK1YGQd0Imc6rz17ipZbkOe5TEK8BaiyLe02Jnrv7l-onBsLBb4plIgxQES6oncBpR9aQLbfRMzlTOo5BkgPo4GLf9OujZ2JZBDLe8lA/http%3A%2F%2Fwww.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:30 To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hipppocampal segmentation on freesurfer
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External Email - Use Caution
Hi experts,
I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass?
Saurabh
________________________________
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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________________________________ 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.
Hard to tell without seeing your data, but it is sometimes the case. You could try running the module on a couple of your worst cases and see what happens. It takes about 30 minutes per case.
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 "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 12:14 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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External Email - Use Caution Okay, so could I expect better segmentation results from that without having adjacent choroid plexus/white matter included as hippocampus.
Saurabh ________________________________ 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: Tuesday, April 20, 2021 11:06 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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If you’re only/mostly interested in the hippocampus, I’d encourage you to try the subfield module 😉
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:39 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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External Email - Use Caution
Hi Eugenio,
This is recon-all (aseg.mgz), and not the subfields. Thanks
Saurabh
________________________________
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: Tuesday, April 20, 2021 10:36 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
* External Email - Caution *
Dear Saurabh,
Is this recon-all (aseg.mgz), or the hippocampal subfield module?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1C0u8xLvDh4rlmpEJA1NgIB9ww1gy1q7aBCCorYzXS_bga3ESZfuxRTmq_f61IYiq-4CVUbbG9oarENS_seMmdRQzwHJ9rCx6Y26tbt-SnIp4cfPTggOGOv88bgGwBuJF0uLYoZOMD5xNNRMSmUYp7FHyA7XvHGsAEcVCM7njP9AlzsrK1YGQd0Imc6rz17ipZbkOe5TEK8BaiyLe02Jnrv7l-onBsLBb4plIgxQES6oncBpR9aQLbfRMzlTOo5BkgPo4GLf9OujZ2JZBDLe8lA/http%3A%2F%2Fwww.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:30 To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hipppocampal segmentation on freesurfer
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Hi experts,
I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass?
Saurabh
________________________________
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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________________________________ 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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Okay, will do that. Do we have a criteria/cut-off for hippocampal inclusion? Like how many non-hippocampal voxels included as hippocampus are okay to pass? And if we don't then could you suggest me on how to go about it? Thanks!
Saurabh
________________________________ 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: Tuesday, April 20, 2021 11:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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Hard to tell without seeing your data, but it is sometimes the case. You could try running the module on a couple of your worst cases and see what happens. It takes about 30 minutes per case.
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1AN9NkqOlvqdQ133jIA53-MsxuZpTTRjCCsIXzGnEPqaZZNb...
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 12:14 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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Okay, so could I expect better segmentation results from that without having adjacent choroid plexus/white matter included as hippocampus.
Saurabh
________________________________
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: Tuesday, April 20, 2021 11:06 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
* External Email - Caution *
If you’re only/mostly interested in the hippocampus, I’d encourage you to try the subfield module ??
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:39 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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Hi Eugenio,
This is recon-all (aseg.mgz), and not the subfields. Thanks
Saurabh
________________________________
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: Tuesday, April 20, 2021 10:36 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
* External Email - Caution *
Dear Saurabh,
Is this recon-all (aseg.mgz), or the hippocampal subfield module?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1AN9NkqOlvqdQ133jIA53-MsxuZpTTRjCCsIXzGnEPqaZZNb...http://secure-web.cisco.com/1C0u8xLvDh4rlmpEJA1NgIB9ww1gy1q7aBCCorYzXS_bga3ESZfuxRTmq_f61IYiq-4CVUbbG9oarENS_seMmdRQzwHJ9rCx6Y26tbt-SnIp4cfPTggOGOv88bgGwBuJF0uLYoZOMD5xNNRMSmUYp7FHyA7XvHGsAEcVCM7njP9AlzsrK1YGQd0Imc6rz17ipZbkOe5TEK8BaiyLe02Jnrv7l-onBsLBb4plIgxQES6oncBpR9aQLbfRMzlTOo5BkgPo4GLf9OujZ2JZBDLe8lA/http%3A%2F%2Fwww.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:30 To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hipppocampal segmentation on freesurfer
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Hi experts,
I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass?
Saurabh
________________________________
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.
________________________________
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.
________________________________
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.
________________________________ 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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Thank you very much Eugenio.
Regards, Saurabh
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jindal, Saurabh jindals@wustl.edu Sent: Tuesday, April 20, 2021 11:54 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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Okay, will do that. Do we have a criteria/cut-off for hippocampal inclusion? Like how many non-hippocampal voxels included as hippocampus are okay to pass? And if we don't then could you suggest me on how to go about it? Thanks!
Saurabh
________________________________ 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: Tuesday, April 20, 2021 11:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
* External Email - Caution *
Hard to tell without seeing your data, but it is sometimes the case. You could try running the module on a couple of your worst cases and see what happens. It takes about 30 minutes per case.
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 12:14 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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Okay, so could I expect better segmentation results from that without having adjacent choroid plexus/white matter included as hippocampus.
Saurabh
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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: Tuesday, April 20, 2021 11:06 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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If you’re only/mostly interested in the hippocampus, I’d encourage you to try the subfield module ??
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:39 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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Hi Eugenio,
This is recon-all (aseg.mgz), and not the subfields. Thanks
Saurabh
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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: Tuesday, April 20, 2021 10:36 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hipppocampal segmentation on freesurfer
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Dear Saurabh,
Is this recon-all (aseg.mgz), or the hippocampal subfield module?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jindal, Saurabh" jindals@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 11:30 To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hipppocampal segmentation on freesurfer
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Hi experts,
I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass?
Saurabh
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freesurfer@nmr.mgh.harvard.edu
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Iglesias Gonzalez, Juan E. -
Jindal, Saurabh