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bioimagesuiteweb / bisweb

This is the repository for the BioImage Suite Web Project
https://bioimagesuiteweb.github.io/webapp/
Apache License 2.0
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Unable to Load Different Atlas into Web Connectivity Viewer #140

Closed nolanrbrady closed 4 months ago

nolanrbrady commented 5 months ago

Hi, I am trying to load a nifti file of the Gordon 2026 atlas into BioImage Suite using the "Advanced -> Import Parcellation Image" option. I don't see any changes in the GUI (i.e it keep showing the atlas as the Shen et al 268 parcellation atlas). I'm not certain if I am uploading the new parcellation incorrectly or if there is an issue with the functionality. Any help you may be able to provide would be greatly appreciated. Thank you!

bioimagesuiteweb commented 5 months ago

Please share a link to the image

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From: Nolan Brady @.> Sent: Tuesday, June 4, 2024 7:43:12 PM To: bioimagesuiteweb/bisweb @.> Cc: Subscribed @.***> Subject: [bioimagesuiteweb/bisweb] Unable to Load Different Atlas into Web Connectivity Viewer (Issue #140)

Hi, I am trying to load a nifti file of the Gordon 2026 atlas into BioImage Suite using the "Advanced -> Import Parcellation Image" option. I don't see any changes in the GUI (i.e it keep showing the atlas as the Shen et al 268 parcellation atlas). I'm not certain if I am uploading the new parcellation incorrectly or if there is an issue with the functionality. Any help you may be able to provide would be greatly appreciated. Thank you!

— Reply to this email directly, view it on GitHubhttps://github.com/bioimagesuiteweb/bisweb/issues/140, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAUZ5HWQDPJBT2BAR3KD65DZFZGJBAVCNFSM6AAAAABIZS7U3OVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMZTINJVGY2DGMQ. You are receiving this because you are subscribed to this thread.Message ID: @.***>

nolanrbrady commented 5 months ago

Hi, Thank you for your response. I am using the nii.gz file from this github repository. https://github.com/brainspaces/gordon333

Looking further into the issue, it seems that in the console I get the following error:

Screenshot 2024-06-11 at 5 27 00 PM

I have tried converting the image to the RAS orientation mentioned in the error message but it doesn't change the error message.

XeniosP commented 4 months ago

Try using this one. It is a stupid little thing -- we expect images to be 181x217x181 (the old MNI size) and newer ones are 182x218x182. I remapped it a bit.

Xenios

On Tue, Jun 11, 2024 at 7:29 PM Nolan Brady @.***> wrote:

Hi, Thank you for your response. I am using the nii.gz file from this github repository. https://github.com/brainspaces/gordon333

Looking further into the issue, it seems that in the console I get the following error: Screenshot.2024-06-11.at.5.27.00.PM.png (view on web) https://github.com/bioimagesuiteweb/bisweb/assets/26473798/88a5258a-298e-409e-b7e8-7876d2765886 I have tried converting the image to the RAS orientation but it doesn't change the error message.

— Reply to this email directly, view it on GitHub https://github.com/bioimagesuiteweb/bisweb/issues/140#issuecomment-2161768151, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJFX66INFZRKQOIWKSQMSGDZG6B4PAVCNFSM6AAAAABIZS7U3OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRRG43DQMJVGE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

nolanrbrady commented 4 months ago

@XeniosP That makes sense, thank you for the help! I'm not sure if you meant to attach something to your message but I'm not seeing an attached image. Would you mind reuploading it? I would do it myself but I'm not familiar with converting between old and new MNI images. Thank you again!

bioimagesuiteweb commented 4 months ago

Could you email me directly @xenophon dot papademetris @yale.edu

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From: Nolan Brady @.> Sent: Friday, June 14, 2024 4:17:57 PM To: bioimagesuiteweb/bisweb @.> Cc: BioImageSuite Web @.>; Comment @.> Subject: Re: [bioimagesuiteweb/bisweb] Unable to Load Different Atlas into Web Connectivity Viewer (Issue #140)

@XeniosPhttps://github.com/XeniosP That makes sense, thank you for the help! I'm not sure if you meant to attach something to your message but I'm not seeing an attached image. Would you mind reuploading it? I would do it myself but I'm not familiar with converting between old and new MNI images. Thank you again!

— Reply to this email directly, view it on GitHubhttps://github.com/bioimagesuiteweb/bisweb/issues/140#issuecomment-2168706124, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAUZ5HWMENFNZWS4NNTCYBTZHNFXLAVCNFSM6AAAAABIZS7U3OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRYG4YDMMJSGQ. You are receiving this because you commented.Message ID: @.***>