decentralized-source-based-morphometry/compspec.json at main · trendscenter/decentralized-source-based-morphometry · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
{
    "meta": {
        "name": "Decentralized Source Based Morphometry",
        "id": "coinstac-dsbm",
        "version": "v1.0.0",
        "compspecVersion": 2,
        "repository": "https://github.com/trendscenter/decentralized-source-based-morphometry",
        "description": "A Demo for Decentralized Source Based Morphometry"
    },
    "computation": {
        "display": {
            "type": "iframe"
        },
        "input": {
            "data": {
                "label": "Data",
                "type": "files",
                "items": [
                    "NiFTI"
                ],
                "extensions": [
                    [
                        "nii"
                    ]
                ],
                "source": "member",
                "order": 1
            },
            "mask": {
                "group": "options",
                "default": "/computation/local_data/mask.nii",
                "label": "Mask Filename",
                "type": "string",
                "source": "owner",
                "tooltip": "Nifti file name to be use as the mask",
                "order": 2
            },
            "scica_template": {
                "group": "options",
                "default": "/computation/local_data/Neuromark_sMRI_1.0_modelorder-30_2x2x2.nii",
                "label": "Spatially Constrained ICA Template Name",
                "type": "string",
                "source": "owner",
                "tooltip": "Nifti file name to be use as the template for spatially constrained ICA",
                "order": 3
            },
            "subsample_nifti_images": {
                "group": "options",
                "default": "false",
                "label": "Perform input nifti subsampling",
                "type": "boolean",
                "source": "owner",
                "tooltip": "true to subsample nifti images else false",
                "order": 4
            },
            "voxel_size": {
                "group": "options",
                "default": "2",
                "label": "Voxel size (subsampling)",
                "type": "number",
                "source": "owner",
                "tooltip": "Voxel size to subsample nifti images",
                "order": 4
            },
            "covariates": {
                "group": "Regression variables",
                "label": "Covariates",
                "type": "csv",
                "items": ["boolean", "number", "string"],
                "source": "member",
                "tooltip": "csv file with nifti file name, covariates information of each subject in a separate line",
                 "order": 5
            },
            "reference_columns": {
                "group": "Regression variables",
                "label": "Regression reference column(s) and value(s)",
                "default": {},
                "type": "object",
                "source": "owner",
                "tooltip": "Used in regression for dummy encoding categorical covariate columns. Required only if specific value(s) should be used for dummy encoding a column(s); Example : { \"reference_column_name\": \"reference_value\" }",
                "order": 6
            },
            "group_col_name": {
                "group": "Regression variables",
                "label": "Patient/Control column name",
                "default": "",
                "type": "string",
                "source": "owner",
                "tooltip": "Column name in the covariates file that contains patients and controls information.",
                "order": 6
            }
        },
        "output": {},
        "type": "docker",
        "dockerImage": "coinstacteam/coinstac-dsbm",
        "command": [
            "python",
            "/computation/local.py"
        ],
        "remote": {
            "type": "docker",
            "dockerImage": "coinstacteam/coinstac-dsbm",
            "command": [
                "python",
                "/computation/remote.py"
            ]
        }
    }
}