Sagittal Slices

[Newtstein]

Hi there!

Thanks so much for making this available for us! I was just wondering how I can incorporate images of brain slices in the sagittal plane.

Thank you for your time!

[petersaj]

Hi - any direction slice should work, you can just rotate the atlas to match the orientation of the slice. Have you had trouble with it?

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On Sat, 14 Aug 2021 at 1:17 am Newtstein ***@***.***> wrote: Hi there! Thanks so much for making this available for us! I was just wondering how I can incorporate images of brain slices in the sagittal plane. Thank you for your time! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEJG4ICH4NFN2HR4PHH4T7DT4WY2HANCNFSM5CEPQK3Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

[Newtstein]

Hi!

Thank you so much for that! It's working now!

I was also wondering whether or not I can align only a portion of the brain. For example, the images I am working with only capture the cerebellum in the sagittal plane. Is there any way this would work?

Thank you again for your immediate help!

[petersaj]

There's no automated way to estimate alignment to partial slices, but if you do the manual alignment step hopefully it should work alright?

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On Sun, Aug 15, 2021 at 4:28 AM Newtstein ***@***.***> wrote: Hi! Thank you so much for that! It's working now! I was also wondering whether or not I can align only a portion of the brain. For example, the images I am working with only capture the cerebellum in the sagittal plane. Is there any way this would work? Thank you again for your immediate help! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEJG4IDQR6MRUCGKMACIXXDT44X7JANCNFSM5CEPQK3Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

[Newtstein]

Hey Andy!

Thanks for that! The manual alignment step worked perfectly.

My apologies for being a novice with MATLAB, but I seem to be encountering this error and cannot figure out how to solve it. Whenever you get the chance, let me know what is wrong.

I sincerely appreciate your help.

Error:

[petersaj]

That function used to come from a different repository ( https://github.com/cortex-lab/allenCCF), but it only used a few functions so I copied them over to remove the dependency. If you pull the current repo and make sure all the folders are in the path it should work now?

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On Tue, Aug 17, 2021 at 10:09 PM Newtstein ***@***.***> wrote: Hey Andy! Thanks for that! The manual alignment step worked perfectly. My apologies for being a novice with MATLAB, but I seem to be encountering this error and cannot figure out how to solve it. Whenever you get the chance, let me know what is wrong. I sincerely appreciate your help. Error: [image: Screen Shot 2021-08-17 at 5 04 31 PM] <https://user-images.githubusercontent.com/87092669/129800399-1f7b5c52-c1ac-4e5b-a7ce-e266a944bc25.png> [image: Screen Shot 2021-08-17 at 5 07 25 PM] <https://user-images.githubusercontent.com/87092669/129800777-b9e3de44-9f8d-4752-9b1d-7542903b92c9.png> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEJG4IDSSNU4633DCDW5DJLT5LFX3ANCNFSM5CEPQK3Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .