jhuguetn/cat12 repository overview

⁠CAT12-docker

Ready-to-use Docker image with the standalone version of the Computational Anatomy Toolbox⁠ (CAT) toolbox for SPM⁠. No MATLAB license required.

• CAT code repository: https://github.com/christianGaser/cat12⁠
• CAT useful commands: https://neuro-jena.github.io/enigma-cat12/#standalone⁠

Find the image in Docker Hub here⁠.

⁠Components

• Ubuntu 20.04 LTS (Focal Fossa)
• MATLAB Compiler Runtime R2017b (version 9.3)
• SPM standalone version (SPM25 25.01.02)
• CAT toolbox (CAT12.9 r2665)

⁠Usage

 docker pull jhuguetn/cat12
 ...
 docker run -v /data:/data jhuguetn/cat12 -b /data/matlab_batch_script.m /data/img.nii

⁠Example (segmentation of T1w image)

 docker run -it --rm -v `pwd`/data:/data jhuguetn/cat12 \
 -b /opt/spm/standalone/cat_standalone_segment.m \
 /data/my_dataset/sub-0001/anat/sub-0001_T1w.nii

⁠Example using singularity (longitudinal segmentation)

You need to make sure to map $HOME/.matlab if you are running in contained mode, because the MCR will write into that folder.

singularity build cat12-latest.sif docker://jhuguetn/cat12:latest
singularity run --cleanenv --contain \
  -B $PWD:/data \
  -B $HOME/.matlab \
  cat12-latest.sif \
  -b /opt/spm/standalone/cat_standalone_segment_long.m /data/my_dataset/sub-01/ses-0{1,2,3}/anat/sub-01_T1w.nii

⁠Credits

Jordi Huguet (BarcelonaBeta Brain Research Center⁠)