FSfslVBM.json

{
    "name": "FSfslVBM",
    "author": "roshchupkin",
    "description": "Small wrapper for running voxel-based morphometry (VBM) based on FreeSurfer segmentation",
    "tool-version": "unknown",
    "url": "https://github.com/roshchupkin/FSfslVBM",
    "descriptor-url": "https://raw.githubusercontent.com/glatard/enigma_shape-docker/master/FSfslVBM.json",
    "schema-version": "0.5",
    "command-line": "chmod 700 [FREESURFER_SUBJECT_DIR]/mri && mkdir -p vbm-results-$(basename [FREESURFER_SUBJECT_DIR]) && bash /opt/FSfslVBM/fsl_vbm_pipeline.sh -i [FREESURFER_SUBJECT_DIR]/mri/aseg.mgz -f /usr/local/freesurfer/ -v /opt/FSfslVBM -o vbm-results-$(basename [FREESURFER_SUBJECT_DIR]) -n $(basename [FREESURFER_SUBJECT_DIR]) -t /opt/FSfslVBM/brain_vbm_atlas.nii.gz -c /opt/FSfslVBM/GM_2_MNI152GM_1mm.cnf",
    "container-image": {
        "image": "glatard/fsfslvbm: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": "vbm-results-[FREESURFER_SUBJECT_DIR]"
        }
    ],
    "tags": {
        "genetics": true,
        "ENIGMA": true
    },
    "suggested-resources": {
        "walltime-estimate": 14400
    }
}