nope, I agree completely. Brainstem and ventralDC and such were never very well-defined by the CMA, which is what our original manual labels were based on. Eugenio's stuff is a significant improvement Bruce On Tue, 26 Jan 2016, Eugenio Iglesias wrote:

Dear Mohamad, The brainstem module uses different anatomical definitions than aseg/wmparc, and yes, the largest discrepancy is in the midbrain. For the midbrain, I like the segmentation from the brainstem module better, since it is based on manual annotations made by UCSF collaborators working explicitly on the brainstem regions. But Bruce's opinion might be different? Cheers, /Eugenio

Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

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From: "Mohamad J. Alshikho" MALSHIKHO@mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, January 26, 2016 4:05:24 PM Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

Dear Freesurfers, After segmenting the brain stem using FS6 tools. I used Free view to visualize the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and "brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by flipping the images. I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an output of brain stem segmentation). I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. Now After segmenting the brain stem. I see that the Ventral DC belongs to the mid brain.

Is this natural?

Thanks in advance for any suggestion!

Mohamad

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Here it is (open access) http://www.sciencedirect.com/science/article/pii/S1053811915001895

Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

From: "Mohamad J. Alshikho" MALSHIKHO@mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, January 26, 2016 4:25:35 PM Subject: Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

Bruce and Juan, Thanks a lot for your quick answer. I have one more question please:

What are the anatomical definitions that the brain stem module uses in order to segment the brain stem. If you can point me to a reference that can help me to understand this point this will be great!!

Thanks again

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.iglesias@bcbl.eu] Sent: Tuesday, January 26, 2016 10:16 AM To: Freesurfer support list Subject: Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

Dear Mohamad, The brainstem module uses different anatomical definitions than aseg/wmparc, and yes, the largest discrepancy is in the midbrain. For the midbrain, I like the segmentation from the brainstem module better, since it is based on manual annotations made by UCSF collaborators working explicitly on the brainstem regions. But Bruce's opinion might be different? Cheers, /Eugenio

Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

From: "Mohamad J. Alshikho" MALSHIKHO@mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, January 26, 2016 4:05:24 PM Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

Dear Freesurfers, After segmenting the brain stem using FS6 tools. I used Free view to visualize the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and "brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by flipping the images. I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an output of brain stem segmentation). I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. Now After segmenting the brain stem. I see that the Ventral DC belongs to the mid brain.

Is this natural?

Thanks in advance for any suggestion!

Mohamad

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.