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ANTsX / ANTs

Advanced Normalization Tools (ANTs)
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ANTs/ANTsR Brain Templates #651

Closed chengaox closed 5 years ago

chengaox commented 5 years ago

Hello, I recently read your paper " Optimal Symmetric Multimodal Templates and Concatenated Random Forests for Supervised Brain Tumor Segmentation (Simplified) with ANTsR".And I am trying to implement ANTs/ANTsR on BRATS 2013 3-D dataset to reproduce your results.

1.I have download the "ANTs/ANTsR Brain Templates" which you provided at figshare include T1 symmetric template. Could you give me some details about how can I get the T2 and flair symmetric template?

2.I have run your 2-D example with input seven brain/tumor tissue labels to creat RF model and get good segmentation result ,but not get a good result with BRATS2013 3-D data .I only input four tumor labels(edema,enhancing tumor...) with the construction of RF model . Is this a wrong input cause my result？How can I get seven brain/tumor tissue labels like your 2-D example? I have no idea about this currently.

Thank you so much!

ntustison commented 5 years ago

Hi,

1) You can download the other modalities from here. Hey @stnava , a couple people have asked about the other modalities so I trie to upload a KirbyMultiModal archive to the ANTs/ANTsR Brain Templates on Figshare but I'm not a collaborator. Can you make me a collaborator or upload this archive? It's only ~250 MB.

2) To get the seven labels for the brats data, I ran the training data through our brain segmentation protocol. Check out the "stages" capabilities of the antsCorticalThickness.sh script. Here's an example.

Nick

stnava commented 5 years ago

i think you are listed as collaborator - but i cant find out how to check this or "upgrade" your status or anything. i will download and add this file though as a stopgap measure.

ntustison commented 5 years ago

Thanks Brian.

chengaox commented 5 years ago

Thank you for your help ! I have get segmentation label of csf ,corticalgm ,wm,deep gm as you suggested with antsCorticalThickness,but how can I mask this segmentation results with provided brats tumor label and finally get the seven labels?

stnava commented 5 years ago

you should open a new issue and ask this question more clearly if you are still wondering.