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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
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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)
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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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