search

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
70 stars 11 forks source link

What is the template of BraTS-toolkit? #16

Closed kyuchoi closed 2 years ago

kyuchoi commented 2 years ago

Hi, I want to use this BraTS-toolkit to preprocess my custom MRI dataset into BraTS-style (i.e. same preprocessing such as 1mm isotropic, and crop or pad into (240, 240, 155) as well as RAS+ orientation). However, I've found that BraTS used the ICBM template (probably MNI152_T1_1mm_Brain.nii.gz ) in the following paper: https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6975210 Is this BraTS-toolkit use the same template to register ? or individually coregsitered to individual contrast-enhanced T1WI space?

Thanks,

neuronflow commented 2 years ago

Hi BTK preprocessor outputs skull-stripped images in both native and brats space.

kyuchoi commented 2 years ago

Thank you for your kind reply. What do you mean by "native" space? You mean the contrast enhanced 3D T1-weighted image, which has the highest resolution among T1WI, T2WI, FLAIR, and CE-T1WI?

Thank you so much!

neuronflow commented 2 years ago

With native space I mean the respective native spaces of T1, T1c, T2, FLAIR.

The manuscript describes the output generation in more detail, in particular figure 2 tries to illustrate it: https://www.frontiersin.org/articles/10.3389/fnins.2020.00125/full