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Good afternoon,
I would like to verify that the subcallosal cingulate cortex (SCC) segmentation of my subjects are correct. I want to do this by creating an average label of the left SCC and an average label of the right SCC which I can then map onto each subject.
If I save these labels from each subject as a volume (.mgz) and then run mri_concat on the left SCC labels (.mgz) and then on the right SCC labels (.mgz), would this accomplish my desired goal?
Tks,
Carlos
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Hi Carlos,
mri_concat concatenates input .mgz files.
The following command will output C.mgz with A.mgz as the first frame, and B.mgz as the second frame, assuming both A and B have only one frame. mri_concat --i A.mgz --i B.mgz --o C.mgz
I’m not sure that is what you are looking for.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Carlos Alcocer Sent: Wednesday, April 19, 2023 1:02 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] creating average labels
External Email - Use Caution Good afternoon,
I would like to verify that the subcallosal cingulate cortex (SCC) segmentation of my subjects are correct. I want to do this by creating an average label of the left SCC and an average label of the right SCC which I can then map onto each subject.
If I save these labels from each subject as a volume (.mgz) and then run mri_concat on the left SCC labels (.mgz) and then on the right SCC labels (.mgz), would this accomplish my desired goal?
Tks,
Carlos
External Email - Use Caution
I am basically looking for a way to create an average of the labels for the L subcallosal cingulate cortex (SCC) and then make an average of the labels for the R SCC across all subjects and use these 2 average labels as a mask to see if the average label L SCC and average label of R SCC aligns well with with the actual location of the L and R SCC for each individual subject. Do you know of a better way to do this?
On Thu, Apr 20, 2023 at 9:19 AM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
External Email - Use CautionHi Carlos,
mri_concat concatenates input .mgz files.
The following command will output C.mgz with A.mgz as the first frame, and B.mgz as the second frame, assuming both A and B have only one frame.
mri_concat --i A.mgz --i B.mgz --o C.mgz
I’m not sure that is what you are looking for.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer *Sent:* Wednesday, April 19, 2023 1:02 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] creating average labels
External Email - Use Caution *Good afternoon,
I would like to verify that the subcallosal cingulate cortex (SCC) segmentation of my subjects are correct. I want to do this by creating an average label of the left SCC and an average label of the right SCC which I can then map onto each subject.
If I save these labels from each subject as a volume (.mgz) and then run mri_concat on the left SCC labels (.mgz) and then on the right SCC labels (.mgz), would this accomplish my desired goal?
Tks,
Carlos
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1woH-7I1iI8jy49UxI2T2XJlNeSSdGVsY4IBFUUGhxOAxPK... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1GS07NEXkXwlLogxjj80mBImEu4X1pw97cO01n0kM2da3QN... < https://secure-web.cisco.com/1GS07NEXkXwlLogxjj80mBImEu4X1pw97cO01n0kM2da3QN... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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What form are your labels in? If in freesurfer .label format, then you can convert them to an annotation (mris_label2annot), then use annot2std to create an average annotation in fsaverage (standard) space using your subject, you can then map the annot to any subject
On 4/20/2023 12:29 PM, Carlos Alcocer wrote:
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I am basically looking for a way to create an average of the labels for the L subcallosal cingulate cortex (SCC) and then make an average of the labels for the R SCC across all subjects and use these 2 average labels as a mask to see if the average label L SCC and average label of R SCC aligns well with with the actual location of the L and R SCC for each individual subject. Do you know of a better way to do this?
On Thu, Apr 20, 2023 at 9:19 AM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
External Email - Use Caution Hi Carlos, mri_concat concatenates input .mgz files. The following command will output C.mgz with A.mgz as the first frame, and B.mgz as the second frame, assuming both A and B have only one frame. mri_concat --i A.mgz --i B.mgz --o C.mgz I’m not sure that is what you are looking for. Best, Yujing *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer *Sent:* Wednesday, April 19, 2023 1:02 PM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] creating average labels * External Email - Use Caution * Good afternoon, I would like to verify that the subcallosal cingulate cortex (SCC) segmentation of my subjects are correct. I want to do this by creating an average label of the left SCC and an average label of the right SCC which I can then map onto each subject. If I save these labels from each subject as a volume (.mgz) and then run mri_concat on the left SCC labels (.mgz) and then on the right SCC labels (.mgz), would this accomplish my desired goal? Tks, Carlos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1VcY9Mv2eUjqIocG6tpRukP8NjnBDrwlBmAu6BwQSf2B4Wcvh6rYgfb-RiADvMB4rsDjtMUMPH1tHFTJt88gJ9M7e9GJK254R2fthJOLrpRt-g56nI_pj08sUlf6CxfFKsgwct1sDs39uuu5ofgF8qk4zx8FSRUQDy0cHI-X8wJLM5iOl6uGFmYiI3Xxikr1Rztu-9YMeLU4JY-VZhQJ3fVqZzf0MNvrQHqi4r9JoamZ-iZDBT4esJo1nA5lGMxSwiKodDr9Q6gT43Dyawur7DA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1woH-7I1iI8jy49UxI2T2XJlNeSSdGVsY4IBFUUGhxOAxPK7rJ8nSKVJaIQhdvMJyQg_9YfQGe9EQPSjhTTNJWBjnmgHgPIBcSyxiXmE833bNWTLnfr7erepKzCqPOTGP6weFblfgkD_cpnX8x4-9AEdLyWgxdI_uN5PzpR3NXxTVj7oQoZsvx1fPEy-WF4xdNiJaDsH9BP-nh5ptcbhDSEDYFFiboC4A96t04BaCdcokiqAiPjgDtWdHVjULN-XH3Xa1U2BT5JqJfj6EE28tBZHDBJmvXeEOUJUdqwFzIkQkGNOSVJmcr6PAfsplHuwp/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1FwN0ZDcbZ5KVrGfWav5tux3jShbGUEyO8BhEjimbBIJLiLnIPiFgWT0TGBiFG-jQKMRuspGin5AiipDzQl2_ZGLFu45tE3MVnXm2zGp55cnQJ7qSQMb5GOvKGWTVjaH8qRdcEihnIBTLr9OaAMVljj-dbgzO_2ZojODqQQAP4ztVLpAT_L9OF-KfU3Fo4uQiRCoyiQRWACWpvxKoX4OqixJvVYBEx7NijdrS7Ne3yH4bdXYFXGG-97GaFqmpxkVOs5-CdmR66Ei6EgkS8n_fxA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/1GS07NEXkXwlLogxjj80mBImEu4X1pw97cO01n0kM2da3QNcGfEj1qXlOdoxCPUN9s3jlIlf_N8V6YQts6uv0jDMCppWabJxFKyXgW_Bfop0OebJAqzh9kaTQ--TB0ZMYPJXcR1CVj1KaHyMA46so_m1sJ0f-yurVRbhM5uGclAHTCYI0yCqj0H5wAJzz4FmKVmJMZGXbb92Bxjlnvpqvtw58dqQ3GuqspGU_QGu4cp4rtf8CSLgcBif9q_YVrnxxfFijOx4ZB4yubtFrvDAVU6EHZcBUKtT2oA4fvUt69KYuP58KWcCZ1T6wQkAQ7uxu/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1FwN0ZDcbZ5KVrGfWav5tux3jShbGUEyO8BhEjimbBIJLiLnIPiFgWT0TGBiFG-jQKMRuspGin5AiipDzQl2_ZGLFu45tE3MVnXm2zGp55cnQJ7qSQMb5GOvKGWTVjaH8qRdcEihnIBTLr9OaAMVljj-dbgzO_2ZojODqQQAP4ztVLpAT_L9OF-KfU3Fo4uQiRCoyiQRWACWpvxKoX4OqixJvVYBEx7NijdrS7Ne3yH4bdXYFXGG-97GaFqmpxkVOs5-CdmR66Ei6EgkS8n_fxA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/1GS07NEXkXwlLogxjj80mBImEu4X1pw97cO01n0kM2da3QNcGfEj1qXlOdoxCPUN9s3jlIlf_N8V6YQts6uv0jDMCppWabJxFKyXgW_Bfop0OebJAqzh9kaTQ--TB0ZMYPJXcR1CVj1KaHyMA46so_m1sJ0f-yurVRbhM5uGclAHTCYI0yCqj0H5wAJzz4FmKVmJMZGXbb92Bxjlnvpqvtw58dqQ3GuqspGU_QGu4cp4rtf8CSLgcBif9q_YVrnxxfFijOx4ZB4yubtFrvDAVU6EHZcBUKtT2oA4fvUt69KYuP58KWcCZ1T6wQkAQ7uxu/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.-- Carlos Alcocer B.A. Neurobiology and Behavior, Cornell University, 2019 818-746-0302
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Carlos Alcocer -
Douglas N. Greve -
Huang, Yujing