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.com<http://www.rcsi.com/>
>>
>>
>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://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.com<http://www.rcsi.com/>
>
>
> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://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
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
RCSI
Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohanlon@rcsi.ie W: www.rcsi.com
Transforming
Healthcare Education, Research and Service: RCSI Strategic Plan
2018-2022
RCSI LEADING THE WORLD TO BETTER
HEALTH
> 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.com<http://www.rcsi.com/>
>>
>>
>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://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.com<http://www.rcsi.com/>
>
>
> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://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