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neuronflow / BraTS-Toolkit

Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript.
https://www.frontiersin.org/articles/10.3389/fnins.2020.00125/full
GNU Affero General Public License v3.0
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Brats template in nii.gz format and brats atlas (template with segmentations of regions of interest) #39

Closed DanielaTalba1 closed 1 year ago

DanielaTalba1 commented 1 year ago

@neuronflow Hello, hope you're good.

please would the template used to register images in bratspace be available in .nii.gz format (240240155) and possibly an atlas of this template with segmented regions of interest?

Thank you for your reply.

Daniela

neuronflow commented 1 year ago

Can you please rephrase your question? I don't understand.

DanielaTalba1 commented 1 year ago

@neuronflow in fact, when we have raw data, we use the brats toolkit to realign this data in brats space. the images obtained after realignment have the shape 240x240x155 in 3D. i'd like to know if the template image used for this realignment, which surely has the dimensions 240x240x155, is available in opensource. ideally it's a nifti template image. And also would there be an atlas, i.e. the template with regions of interest already segmented as well.

Thank you

neuronflow commented 1 year ago

You can find the BraTS atlas here with BrainLes preprocessing: https://github.com/BrainLesion/preprocessing/tree/main/brainles_preprocessing/registration/atlas

BTK uses the same atlas, which is the SRI 24 atlas. I am not aware of brain region annotations for this atlas, please let me know if you find some. I would not be surprised if they exist :)

DanielaTalba1 commented 1 year ago

@neuronflow thank you for your quick reply.