shape_group_run.json

{
    "name": "shape_group_run",
    "author": "ENIGMA",
    "description": "This tool takes FreeSurfer aseg.mgz files and generates homologous mesh representations of subcortical ROI boundaries and vertex-wise shape features for statistical analysis. Please cite the following work when using this tool: 1. Gutman, B.A., Madsen, S.K., Toga, A.W., Thompson, P.M.: A Family of Fast Spherical Registration Algorithms for Cortical Shapes. In: Multimodal Brain Image Analysis, vol. 8159, pp. 246-257. Springer International Publishing (2013) 2. Gutman, B.A., Wang, Y., Rajagopalan, P., Toga, A.W., Thompson, P.M.: Shape matching with medial curves and 1-D group-wise registration. In: Biomedical Imaging (ISBI), 2012 9th IEEE International Symposium on, pp. 716-719. (2012)",
    "tool-version": "unknown",
    "descriptor-url": "https://raw.githubusercontent.com/glatard/enigma_shape-docker/master/shape_group_run.json",
    "schema-version": "0.5",
    "command-line": "chmod 700 [FREESURFER_SUBJECT_DIR]/mri && echo $(basename [FREESURFER_SUBJECT_DIR]) > ids.csv && shape_group_run.sh ids.csv $(dirname [FREESURFER_SUBJECT_DIR]) shape-results-[FREESURFER_SUBJECT_DIR]",
    "container-image": {
        "image": "glatard/enigma_shape:latest",
        "type": "docker"
    },
    "online-platform-urls": [
        "https://portal.cbrain.mcgill.ca"
    ],
    "inputs": [
        {
            "id": "freesurfer_subject_dir",
            "name": "Freesurfer subject output directory",
            "description": "A Freesurfer subject output directory, usually named after a subject id (e.g., '12345').",
            "type": "File",
            "value-key": "[FREESURFER_SUBJECT_DIR]"
        }
    ],
    "output-files": [
        {
            "id": "outputs",
            "name": "Output directory",
            "path-template": "shape-results-[FREESURFER_SUBJECT_DIR]"
        }
    ],
    "tags": {
        "genetics": true,
        "ENIGMA": true
    },
    "suggested-resources": {
        "walltime-estimate": 3600
    },
    "doi": "10.5281/zenodo.3736815"
}