Installation

CortPro is designed to run within containerised environments to simplify dependency management. The toolbox relies on the micapipe container, along with FreeSurfer and Singularity.

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System requirements

• Operating system: Linux or MacOS

• Hardware: multi-core CPU; GPU optional (for FastSurfer acceleration)

• Disk space: depends on input MRI resolution and number of subjects

• Memory: 16 GB RAM recommended

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Dependencies

To run CortPro, you will need:

1. Singularity

   • Must be installed and available on $PATH.

   • See official installation instructions.

2. FreeSurfer

   • Required for cortical surface reconstruction and alignment procedures.

   • A valid license.txt must be present in your FreeSurfer directory.

   • See download and installation instriuctions > <https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall>

3. Singularity images

   • Required container: cortpro.sif (see how to download below).

   • Optional container: fastsurfer_gpu.sif (for when FreeSurfer outputs are missing).

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Quick setup

1. Clone the repository

git clone https://github.com/yourusername/CortPro.git
cd CortPro

2. Set up environment variables

Make sure your environment can find FreeSurfer. For example:

# depends on your system, but for example:
module load freesurfer/7.4
export FREESURFER_HOME=/opt/freesurfer/7.4/
source $FREESURFER_HOME/SetUpFreeSurfer.sh

3. Download containers

# provide the location of your singularity images
sing_dir=/data/singularity

# download the cortpro image
singularity pull ${sing_dir}/cortpro.sif docker://ghcr.io/caseypaquola/cortpro:latest

# ensure cortpro.sif and (optional) fastsurfer_gpu.sif are present in the directory
ls -l $sing_dir

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Verifying installation

After setup, try running the help command:

./microstructure_profiling.sh --help

If the script runs and prints the usage information, your installation is complete 🎉

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Troubleshooting

• Singularity not found → Ensure it is installed and available on your $PATH.

• FreeSurfer license error → Place a valid license.txt inside your FreeSurfer directory.

• Container not found → Check that cortpro.sif is in the directory specified by --sing-dir.

• GPU errors with FastSurfer → Confirm CUDA drivers are correctly installed and match your hardware.

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Next steps

• Learn how to run the pipeline in usage