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Hello Bruce,

Yes, i do want segmentation. But i am more interested in getting just white matter and grey matter in segmented brain. As the segmentation results also have left ventricles and right ventricles and other parts as well. I am more interested in just getting white matter + grey matter of brain. How can i get this ?

Also, I looked at aparc+aseg.mgz, when i try to see 3D of it, using free-view. I see half brain in 3D. How can i see the 3D of segmented brain.

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 30, 2018 7:26:37 PM Subject: Re: [Freesurfer] white matter and grey matter

Hi Ritesh

can you clarify what you mean? Do you want a segmentation? You can get that in the aparc+aseg.mgz at the end of the recon-all processing.

cheers Bruce On Wed, 30 May 2018, Ritesh Mahajan wrote:

   External Email - Use Caution

Hello Team,

1. How can i just get the white matter and grey matter together?
2. At what stage of free-surfer i can get this?

I tried looking at the brainmask.mgz at the end of recon-all -autorecon1 stage. But, it looks like it has CSF and other parts of brain as well.

Can you please help me out with this?

Thanks, Ritesh Mahajan

---

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

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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.

External Email - Use Caution

Thank you Bruce. This really helped.

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 31, 2018 6:40:16 PM Subject: Re: [Freesurfer] white matter and grey matter

Hi Ritesh

Ruopeng can help you with freeview, but you can always extract any set of labels from the aparc+aseg and binarize them if you wish (mri_extract_lables, mri_binarize)

cheers Bruce On Thu, 31 May 2018, Ritesh Mahajan wrote:

   External Email - Use Caution

Hello Bruce,

Yes, i do want segmentation. But i am more interested in getting just white matter and grey matter in segmented brain. As the segmentation results also have left ventricles and right ventricles and other parts as well. I am more interested in just getting white matter + grey matter of brain. How can i get this ?

Also, I looked at aparc+aseg.mgz, when i try to see 3D of it, using free-view. I see half brain in 3D. How can i see the 3D of segmented brain.

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 30, 2018 7:26:37 PM Subject: Re: [Freesurfer] white matter and grey matter

Hi Ritesh

can you clarify what you mean? Do you want a segmentation? You can get that in the aparc+aseg.mgz at the end of the recon-all processing.

cheers Bruce On Wed, 30 May 2018, Ritesh Mahajan wrote:

...

   External Email - Use Caution

Hello Team,

1. How can i just get the white matter and grey matter together?
2. At what stage of free-surfer i can get this?

I tried looking at the brainmask.mgz at the end of recon-all -autorecon1 stage. But, it looks like it has CSF and other parts of brain as well.

Can you please help me out with this?

Thanks, Ritesh Mahajan

---

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

---

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.

---

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

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