Snakemake workflow: smk-epilepsy-7T-sctx

Snakemake workflow for processing BIDSified 7T MRI data as described in "Multi-scale structural alterations of basal ganglia in focal epilepsy as demonstrated by 7T MRI" (link here)

💽 Inputs:

• participants.tsv file with target subject IDs for both controls (prefixed with C, e.g., sub-C001) and patients.
• For each subject:
  • BIDS dataset that includes
    • B1+ map
    • MP2RAGE data
  • Demographic and patient info

💻 Singularity containers required:

• Gradient-distortion correction (https://hub.docker.com/r/khanlab/gradcorrect)
• fMRIPrep (https://hub.docker.com/r/nipreps/fmriprep)
• Connectome Workbench (https://hub.docker.com/r/khanlab/connectome-workbench)
• Surfmorph (https://hub.docker.com/r/khanlab/surfmorph)
• FSL

🔒 Also required:

• MATLAB

Python packages that are used

• Numpy
• Pandas
• Nibabel
• PyVista

External scripts that are used

• PreSurfer is developed by Sriranga Kashyap (@srikash). You can download and cite from here: https://doi.org/10.5281/zenodo.4626841.

• More info on the 7T-AMI atlas can be found in the original paper: "Automatic segmentation of deep grey nuclei using a high-resolution 7T magnetic resonance imaging atlas - Quantification of T1 values in healthy volunteers" (https://doi.org/10.1111/ejn.15575). A recipe to build a Singularity can be found here: https://github.com/AlexandreCABANE/7TAMI_MALF

• THOMAS is developed by Manoj Saranathan. You can find the original code here: https://github.com/thalamicseg/thomas_new

• Surfmorph is developed by Ali Khan (@akhanf). You can find the original code here: https://github.com/khanlab/surfmorph

Authors

• Roy AM Haast @royhaast
• Hugo Dary