Hi Madhura,

I'm not sure I understand. The ?h.white is the boundary. If you want to create a voxel representation of it you can use mris_fill

cheers Bruce On Wed, 15 Dec 2010, Ingalhalikar, Madhura wrote:

Bruce and Allison, Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct solution. I just need the labeled WM boundary (ribbon) to seed my fiber tracking. So basically I will have to compute the boundary from wmparc.mgz. Is there anything that does that already? Thanks, Madhura

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 12/10/2010 8:13 PM To: Ingalhalikar, Madhura Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM parcelleted boundary

Hi Madhura,

have you looked at the wmparc.mgz? It might be exactly what you want

Bruce

On Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:

...

Hi,

Is there a way to get the cortical parcellations projected onto the WM boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber tracking. Please let me know,

Thank you, Madhura

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

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yes, the cortical labels in the .annot files apply the ?h.white surfaces

cheers Bruce On Wed, 15 Dec 2010, Ingalhalikar, Madhura wrote:

Bruce, I agree that ?h.white is a boundary. But it is labeled based on cortical labels? If yes, that is exactly what I need. Let me know,

Thanks for your response. Madhura

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 12/15/2010 11:05 AM To: Ingalhalikar, Madhura Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WM parcelleted boundary

Hi Madhura,

I'm not sure I understand. The ?h.white is the boundary. If you want to create a voxel representation of it you can use mris_fill

cheers Bruce On Wed, 15 Dec 2010, Ingalhalikar, Madhura wrote:

...

Bruce and Allison, Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct solution. I just need the labeled WM boundary (ribbon) to seed my fiber tracking. So basically I will have to compute the boundary from wmparc.mgz. Is there anything that does that already? Thanks, Madhura

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 12/10/2010 8:13 PM To: Ingalhalikar, Madhura Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM parcelleted boundary

Hi Madhura,

have you looked at the wmparc.mgz? It might be exactly what you want

Bruce

On Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:

...

Hi,

Is there a way to get the cortical parcellations projected onto the WM boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber tracking. Please let me know,

Thank you, Madhura

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

---

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The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

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Yes, that seems reasonable Bruce

On Dec 15, 2010, at 1:57 PM, "Ingalhalikar, Madhura" Madhura.Ingalhalikar@uphs.upenn.edu wrote:

Bruce,

Please ignore my earlier email. Let me explain what I exactly need. The wmparc.mgz gives me WM parcellation based on cortical parcellation. What I need is just the boundary voxels from wmparc.mgz, such that each voxel in my output has a neighbor in GM and other WM voxels are set to 0. If there is already something available, that would be great. Otherwise I was thinking of proceeding in the following manner,

Input: WMparc.mgz, WM mask, GM mask. Check if each voxel in WMparc.mgz is inside WM mask. If yes, check if the voxel has atleast one neighbor in GM. If yes, set this voxel as output. else, Output is 0.

I hope it makes sense,

Madhura

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 12/15/2010 11:05 AM To: Ingalhalikar, Madhura Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WM parcelleted boundary

Hi Madhura,

I'm not sure I understand. The ?h.white is the boundary. If you want to create a voxel representation of it you can use mris_fill

cheers Bruce On Wed, 15 Dec 2010, Ingalhalikar, Madhura wrote:

...

Bruce and Allison, Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct solution. I just need the labeled WM boundary (ribbon) to seed my fiber tracking. So basically I will have to compute the boundary from wmparc.mgz. Is there anything that does that already? Thanks, Madhura

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 12/10/2010 8:13 PM To: Ingalhalikar, Madhura Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM parcelleted boundary

Hi Madhura,

have you looked at the wmparc.mgz? It might be exactly what you want

Bruce

On Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:

...

Hi,

Is there a way to get the cortical parcellations projected onto the WM boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber tracking. Please let me know,

Thank you, Madhura

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

---

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.

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.