Extract the entorhinal cortex as a mask

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Erik O'Hanlon

12 Jun 2018 12 Jun '18

9:11 a.m.

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Hi FS experts ,

I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward

Thanks for any advice

Best regards

Erik

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

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Bruce Fischl

12 Jun 12 Jun

9:56 a.m.

Hi Erik

yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC as a volume mask

cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

...

   External Email - Use Caution
Hi FS experts ,

I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward

Thanks for any advice

Best regards

Erik

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

Erik O'Hanlon

12:28 p.m.

External Email - Use Caution

Hi Bruce,

Thanks. So if I use the following command

mri_extract_Label aparc+aseg.mgz 216 EC.mgz

would that give me both L and right EC extracted? is there any way to get the left and right separately?

Thanks so much for the help

cheers

Erik

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 12 June 2018 14:56:41 To: Freesurfer support list Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask

Hi Erik

yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC as a volume mask

cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

...

   External Email - Use Caution
Hi FS experts ,

I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward

Thanks for any advice

Best regards

Erik

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

_______________________________________________ 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.

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

Bruce Fischl

2:04 p.m.

I think you can use 1006 (left) and 2006 (right)

cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

...

   External Email - Use Caution
Hi Bruce,

Thanks. So if I use the following command

mri_extract_Label aparc+aseg.mgz 216 EC.mgz

would that give me both L and right EC extracted? is there any way to get the left and right separately?

Thanks so much for the help

cheers

Erik

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 12 June 2018 14:56:41 To: Freesurfer support list Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask

Hi Erik

yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC as a volume mask

cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

...
   External Email - Use Caution
Hi FS experts ,

I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward

Thanks for any advice

Best regards

Erik

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
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.

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

Erik O'Hanlon

13 Jun 13 Jun

7:19 a.m.

External Email - Use Caution

Sorry Bruce,

Yep Thanks. I didn't spot that label just the 216. Worked perfectly.

Thanks again

Erik

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 12 June 2018 19:04:32 To: Freesurfer support list Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask

I think you can use 1006 (left) and 2006 (right)

cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

...

   External Email - Use Caution
Hi Bruce,

Thanks. So if I use the following command

mri_extract_Label aparc+aseg.mgz 216 EC.mgz

would that give me both L and right EC extracted? is there any way to get the left and right separately?

Thanks so much for the help

cheers

Erik

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

...

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 12 June 2018 14:56:41 To: Freesurfer support list Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask

Hi Erik

yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC as a volume mask

cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

...
   External Email - Use Caution
Hi FS experts ,

I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward

Thanks for any advice

Best regards

Erik

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
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.

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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

Bruce Fischl

9:45 a.m.

glad to hear it Bruce On Wed, 13 Jun 2018, Erik O'Hanlon wrote:

...

   External Email - Use Caution
Sorry Bruce,

Yep Thanks. I didn't spot that label just the 216. Worked perfectly.

Thanks again

Erik

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 12 June 2018 19:04:32 To: Freesurfer support list Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask

I think you can use 1006 (left) and 2006 (right)

cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

...
   External Email - Use Caution
Hi Bruce,

Thanks. So if I use the following command

mri_extract_Label aparc+aseg.mgz 216 EC.mgz

would that give me both L and right EC extracted? is there any way to get the left and right separately?

Thanks so much for the help

cheers

Erik
Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 12 June 2018 14:56:41 To: Freesurfer support list Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask

Hi Erik

yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC as a volume mask

cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

...
   External Email - Use Caution
Hi FS experts ,

I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it's straightforward

Thanks for any advice

Best regards

Erik

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
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.

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Bruce Fischl
Erik O'Hanlon