Shell routines segmenting the brain in different volumes, according to a anatomic atlas, and computing volumes statistic, in the subject native space for the grey and white matter.
For a in depth explaination we invite to consult the following reference from Toro et al.
Those scripts are optimize for a BrainVisa files architecture. If you don't use this architecture, please modify the variable common_path accordingly to yours.
You will a brain atlas in the .nii format, in the normalized space. You will also need a lobar atlas, in the fixed (normalized) space.
You will need to have on your machine the following software:
- Matlab, at least the R2014a release with the toolbox SPM12.
- The AIMS functions from the BrainVisa environment need to be available.
- Python, at least the 3.5 Release.
The only script to execute is the pipeline_launcher.sh scripts. In this scripts, you will have to changes the data access path, to your image database, lobar atlas, and anatomical atlas. You'll have to change the path to the scripts folder too. The results will be created in a Roblob folder inside each subject folder with all the sub-folder corresponding to each step of the pipelines. I encourage you to check each step.