9.3.1. Configs

Juseless

Custom DataGrabbers for FZJ INM-7’s beloved juseless.

enum junifer.configs.juseless.datagrabbers.IXISite(value)

Accepted IXI sites.

Member Type:

str

Valid values are as follows:

Guys = <IXISite.Guys: 'Guys'>

HH = <IXISite.HH: 'HH'>

IOP = <IXISite.IOP: 'IOP'>

pydantic model junifer.configs.juseless.datagrabbers.JuselessDataladAOMICID1000VBM

Concrete implementation for Juseless AOMIC ID1000 VBM data fetching.

Implements a DataGrabber to access the AOMIC ID1000 VBM data in Juseless.

Parameters:

datadirpathlib.Path, optional

That path where the datalad dataset will be cloned. If not specified, the datalad dataset will be cloned into a temporary directory.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Show JSON schema

{
   "title": "JuselessDataladAOMICID1000VBM",
   "description": "Concrete implementation for Juseless AOMIC ID1000 VBM data fetching.\n\nImplements a DataGrabber to access the AOMIC ID1000 VBM data in Juseless.\n\nParameters\n----------\ndatadir : pathlib.Path, optional\n    That path where the datalad dataset will be cloned.\n    If not specified, the datalad dataset will be cloned into a temporary\n    directory.",
   "type": "object",
   "properties": {
      "types": {
         "default": [
            "VBM_GM"
         ],
         "items": {
            "const": "VBM_GM",
            "type": "string"
         },
         "title": "Types",
         "type": "array"
      },
      "datadir": {
         "format": "path",
         "title": "Datadir",
         "type": "string"
      },
      "patterns": {
         "additionalProperties": {
            "anyOf": [
               {
                  "additionalProperties": {
                     "anyOf": [
                        {
                           "type": "string"
                        },
                        {
                           "additionalProperties": {
                              "type": "string"
                           },
                           "type": "object"
                        },
                        {
                           "items": {
                              "additionalProperties": {
                                 "type": "string"
                              },
                              "type": "object"
                           },
                           "type": "array"
                        }
                     ]
                  },
                  "type": "object"
               },
               {
                  "items": {
                     "additionalProperties": {
                        "type": "string"
                     },
                     "type": "object"
                  },
                  "type": "array"
               }
            ]
         },
         "default": {
            "VBM_GM": {
               "pattern": "{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz",
               "space": "IXI549Space"
            }
         },
         "title": "Patterns",
         "type": "object"
      },
      "replacements": {
         "default": [
            "subject"
         ],
         "items": {
            "type": "string"
         },
         "title": "Replacements",
         "type": "array"
      },
      "confounds_format": {
         "anyOf": [
            {
               "$ref": "#/$defs/ConfoundsFormat"
            },
            {
               "type": "null"
            }
         ],
         "default": null
      },
      "partial_pattern_ok": {
         "default": false,
         "title": "Partial Pattern Ok",
         "type": "boolean"
      },
      "uri": {
         "default": "https://gin.g-node.org/felixh/ds003097_ReproVBM",
         "format": "uri",
         "maxLength": 2083,
         "minLength": 1,
         "title": "Uri",
         "type": "string"
      },
      "rootdir": {
         "default": ".",
         "format": "path",
         "title": "Rootdir",
         "type": "string"
      },
      "datalad_dirty": {
         "default": false,
         "title": "Datalad Dirty",
         "type": "boolean"
      },
      "datalad_commit_id": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Datalad Commit Id"
      },
      "datalad_id": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Datalad Id"
      }
   },
   "$defs": {
      "ConfoundsFormat": {
         "description": "Accepted confounds format.",
         "enum": [
            "fmriprep",
            "adhoc"
         ],
         "title": "ConfoundsFormat",
         "type": "string"
      }
   },
   "additionalProperties": true
}

Config:

• use_enum_values: bool = True

• extra: str = allow

Fields:

• patterns (dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]])

• replacements (list[str])

• types (list[Literal[junifer.datagrabber.base.DataType.VBM_GM]])

• uri (pydantic.networks.HttpUrl)

Validators:

field patterns: dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]] = {'VBM_GM': {'pattern': '{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz', 'space': 'IXI549Space'}}

field replacements: list[str] = ['subject']

field types: list[Literal[DataType.VBM_GM]] = [<DataType.VBM_GM: 'VBM_GM'>]

field uri: HttpUrl = HttpUrl('https://gin.g-node.org/felixh/ds003097_ReproVBM')

model_post_init(context)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

pydantic model junifer.configs.juseless.datagrabbers.JuselessDataladCamCANVBM

Concrete implementation for Juseless CamCAN VBM data fetching.

Implements a DataGrabber to access the CamCAN VBM data in Juseless.

Parameters:

datadirpathlib.Path, optional

That path where the datalad dataset will be cloned. If not specified, the datalad dataset will be cloned into a temporary directory.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Show JSON schema

{
   "title": "JuselessDataladCamCANVBM",
   "description": "Concrete implementation for Juseless CamCAN VBM data fetching.\n\nImplements a DataGrabber to access the CamCAN VBM data in Juseless.\n\nParameters\n----------\ndatadir : pathlib.Path, optional\n    That path where the datalad dataset will be cloned.\n    If not specified, the datalad dataset will be cloned into a temporary\n    directory.",
   "type": "object",
   "properties": {
      "types": {
         "default": [
            "VBM_GM"
         ],
         "items": {
            "const": "VBM_GM",
            "type": "string"
         },
         "title": "Types",
         "type": "array"
      },
      "datadir": {
         "format": "path",
         "title": "Datadir",
         "type": "string"
      },
      "patterns": {
         "additionalProperties": {
            "anyOf": [
               {
                  "additionalProperties": {
                     "anyOf": [
                        {
                           "type": "string"
                        },
                        {
                           "additionalProperties": {
                              "type": "string"
                           },
                           "type": "object"
                        },
                        {
                           "items": {
                              "additionalProperties": {
                                 "type": "string"
                              },
                              "type": "object"
                           },
                           "type": "array"
                        }
                     ]
                  },
                  "type": "object"
               },
               {
                  "items": {
                     "additionalProperties": {
                        "type": "string"
                     },
                     "type": "object"
                  },
                  "type": "array"
               }
            ]
         },
         "default": {
            "VBM_GM": {
               "pattern": "{subject}/mri/m0wp1{subject}.nii.gz",
               "space": "IXI549Space"
            }
         },
         "title": "Patterns",
         "type": "object"
      },
      "replacements": {
         "default": [
            "subject"
         ],
         "items": {
            "type": "string"
         },
         "title": "Replacements",
         "type": "array"
      },
      "confounds_format": {
         "anyOf": [
            {
               "$ref": "#/$defs/ConfoundsFormat"
            },
            {
               "type": "null"
            }
         ],
         "default": null
      },
      "partial_pattern_ok": {
         "default": false,
         "title": "Partial Pattern Ok",
         "type": "boolean"
      },
      "uri": {
         "default": "ria+http://cat_12.5.ds.inm7.de#a139b26a-8406-11ea-8f94-a0369f287950",
         "format": "uri",
         "maxLength": 2083,
         "minLength": 1,
         "title": "Uri",
         "type": "string"
      },
      "rootdir": {
         "default": ".",
         "format": "path",
         "title": "Rootdir",
         "type": "string"
      },
      "datalad_dirty": {
         "default": false,
         "title": "Datalad Dirty",
         "type": "boolean"
      },
      "datalad_commit_id": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Datalad Commit Id"
      },
      "datalad_id": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Datalad Id"
      }
   },
   "$defs": {
      "ConfoundsFormat": {
         "description": "Accepted confounds format.",
         "enum": [
            "fmriprep",
            "adhoc"
         ],
         "title": "ConfoundsFormat",
         "type": "string"
      }
   },
   "additionalProperties": true
}

Config:

• use_enum_values: bool = True

• extra: str = allow

Fields:

• patterns (dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]])

• replacements (list[str])

• types (list[Literal[junifer.datagrabber.base.DataType.VBM_GM]])

• uri (pydantic.networks.HttpUrl)

Validators:

field patterns: dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]] = {'VBM_GM': {'pattern': '{subject}/mri/m0wp1{subject}.nii.gz', 'space': 'IXI549Space'}}

field replacements: list[str] = ['subject']

field types: list[Literal[DataType.VBM_GM]] = [<DataType.VBM_GM: 'VBM_GM'>]

field uri: HttpUrl = 'ria+http://cat_12.5.ds.inm7.de#a139b26a-8406-11ea-8f94-a0369f287950'

model_post_init(context)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

pydantic model junifer.configs.juseless.datagrabbers.JuselessDataladIXIVBM

Concrete implementation for Juseless IXI VBM data fetching.

Implements a DataGrabber to access the IXI VBM data in Juseless.

Parameters:

datadirpathlib.Path, optional

That path where the datalad dataset will be cloned. If not specified, the datalad dataset will be cloned into a temporary directory.

siteslist of IXISite, optional

IXI sites. By default, all available sites are selected.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Show JSON schema

{
   "title": "JuselessDataladIXIVBM",
   "description": "Concrete implementation for Juseless IXI VBM data fetching.\n\nImplements a DataGrabber to access the IXI VBM data in Juseless.\n\nParameters\n----------\ndatadir : pathlib.Path, optional\n    That path where the datalad dataset will be cloned.\n    If not specified, the datalad dataset will be cloned into a temporary\n    directory.\nsites : list of :enum:`.IXISite`, optional\n    IXI sites.\n    By default, all available sites are selected.",
   "type": "object",
   "properties": {
      "types": {
         "default": [
            "VBM_GM"
         ],
         "items": {
            "const": "VBM_GM",
            "type": "string"
         },
         "title": "Types",
         "type": "array"
      },
      "datadir": {
         "format": "path",
         "title": "Datadir",
         "type": "string"
      },
      "patterns": {
         "additionalProperties": {
            "anyOf": [
               {
                  "additionalProperties": {
                     "anyOf": [
                        {
                           "type": "string"
                        },
                        {
                           "additionalProperties": {
                              "type": "string"
                           },
                           "type": "object"
                        },
                        {
                           "items": {
                              "additionalProperties": {
                                 "type": "string"
                              },
                              "type": "object"
                           },
                           "type": "array"
                        }
                     ]
                  },
                  "type": "object"
               },
               {
                  "items": {
                     "additionalProperties": {
                        "type": "string"
                     },
                     "type": "object"
                  },
                  "type": "array"
               }
            ]
         },
         "default": {
            "VBM_GM": {
               "pattern": "{site}/{subject}/mri/m0wp1{subject}.nii.gz",
               "space": "IXI549Space"
            }
         },
         "title": "Patterns",
         "type": "object"
      },
      "replacements": {
         "default": [
            "site",
            "subject"
         ],
         "items": {
            "type": "string"
         },
         "title": "Replacements",
         "type": "array"
      },
      "confounds_format": {
         "anyOf": [
            {
               "$ref": "#/$defs/ConfoundsFormat"
            },
            {
               "type": "null"
            }
         ],
         "default": null
      },
      "partial_pattern_ok": {
         "default": false,
         "title": "Partial Pattern Ok",
         "type": "boolean"
      },
      "uri": {
         "default": "ria+http://cat_12.5.ds.inm7.de#b7107c52-8408-11ea-89c6-a0369f287950",
         "format": "uri",
         "maxLength": 2083,
         "minLength": 1,
         "title": "Uri",
         "type": "string"
      },
      "rootdir": {
         "default": ".",
         "format": "path",
         "title": "Rootdir",
         "type": "string"
      },
      "datalad_dirty": {
         "default": false,
         "title": "Datalad Dirty",
         "type": "boolean"
      },
      "datalad_commit_id": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Datalad Commit Id"
      },
      "datalad_id": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Datalad Id"
      },
      "sites": {
         "default": [
            "Guys",
            "HH",
            "IOP"
         ],
         "items": {
            "$ref": "#/$defs/IXISite"
         },
         "title": "Sites",
         "type": "array"
      }
   },
   "$defs": {
      "ConfoundsFormat": {
         "description": "Accepted confounds format.",
         "enum": [
            "fmriprep",
            "adhoc"
         ],
         "title": "ConfoundsFormat",
         "type": "string"
      },
      "IXISite": {
         "description": "Accepted IXI sites.",
         "enum": [
            "Guys",
            "HH",
            "IOP"
         ],
         "title": "IXISite",
         "type": "string"
      }
   },
   "additionalProperties": true
}

Config:

• use_enum_values: bool = True

• extra: str = allow

Fields:

• patterns (dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]])

• replacements (list[str])

• sites (list[junifer.configs.juseless.datagrabbers.ixi_vbm.IXISite])

• types (list[Literal[junifer.datagrabber.base.DataType.VBM_GM]])

• uri (pydantic.networks.HttpUrl)

Validators:

field patterns: dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]] = {'VBM_GM': {'pattern': '{site}/{subject}/mri/m0wp1{subject}.nii.gz', 'space': 'IXI549Space'}}

field replacements: list[str] = ['site', 'subject']

field sites: list[IXISite] = [IXISite.Guys, IXISite.HH, IXISite.IOP]

field types: list[Literal[DataType.VBM_GM]] = [<DataType.VBM_GM: 'VBM_GM'>]

field uri: HttpUrl = 'ria+http://cat_12.5.ds.inm7.de#b7107c52-8408-11ea-89c6-a0369f287950'

model_post_init(context)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

pydantic model junifer.configs.juseless.datagrabbers.JuselessDataladUKBVBM

Concrete implementation for Juseless UKB VBM data fetching.

Implements a DataGrabber to access the UKB VBM data in Juseless.

Parameters:

datadirpathlib.Path, optional

That path where the datalad dataset will be cloned. If not specified, the datalad dataset will be cloned into a temporary directory.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Show JSON schema

{
   "title": "JuselessDataladUKBVBM",
   "description": "Concrete implementation for Juseless UKB VBM data fetching.\n\nImplements a DataGrabber to access the UKB VBM data in Juseless.\n\nParameters\n----------\ndatadir : pathlib.Path, optional\n    That path where the datalad dataset will be cloned.\n    If not specified, the datalad dataset will be cloned into a temporary\n    directory.",
   "type": "object",
   "properties": {
      "types": {
         "default": [
            "VBM_GM"
         ],
         "items": {
            "const": "VBM_GM",
            "type": "string"
         },
         "title": "Types",
         "type": "array"
      },
      "datadir": {
         "format": "path",
         "title": "Datadir",
         "type": "string"
      },
      "patterns": {
         "additionalProperties": {
            "anyOf": [
               {
                  "additionalProperties": {
                     "anyOf": [
                        {
                           "type": "string"
                        },
                        {
                           "additionalProperties": {
                              "type": "string"
                           },
                           "type": "object"
                        },
                        {
                           "items": {
                              "additionalProperties": {
                                 "type": "string"
                              },
                              "type": "object"
                           },
                           "type": "array"
                        }
                     ]
                  },
                  "type": "object"
               },
               {
                  "items": {
                     "additionalProperties": {
                        "type": "string"
                     },
                     "type": "object"
                  },
                  "type": "array"
               }
            ]
         },
         "default": {
            "VBM_GM": {
               "pattern": "m0wp1{subject}_ses-{session}_T1w.nii.gz",
               "space": "IXI549Space"
            }
         },
         "title": "Patterns",
         "type": "object"
      },
      "replacements": {
         "default": [
            "subject",
            "session"
         ],
         "items": {
            "type": "string"
         },
         "title": "Replacements",
         "type": "array"
      },
      "confounds_format": {
         "anyOf": [
            {
               "$ref": "#/$defs/ConfoundsFormat"
            },
            {
               "type": "null"
            }
         ],
         "default": null
      },
      "partial_pattern_ok": {
         "default": false,
         "title": "Partial Pattern Ok",
         "type": "boolean"
      },
      "uri": {
         "default": "ria+http://ukb.ds.inm7.de#~cat_m0wp1",
         "format": "uri",
         "maxLength": 2083,
         "minLength": 1,
         "title": "Uri",
         "type": "string"
      },
      "rootdir": {
         "default": "m0wp1",
         "format": "path",
         "title": "Rootdir",
         "type": "string"
      },
      "datalad_dirty": {
         "default": false,
         "title": "Datalad Dirty",
         "type": "boolean"
      },
      "datalad_commit_id": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Datalad Commit Id"
      },
      "datalad_id": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Datalad Id"
      }
   },
   "$defs": {
      "ConfoundsFormat": {
         "description": "Accepted confounds format.",
         "enum": [
            "fmriprep",
            "adhoc"
         ],
         "title": "ConfoundsFormat",
         "type": "string"
      }
   },
   "additionalProperties": true
}

Config:

• use_enum_values: bool = True

• extra: str = allow

Fields:

• patterns (dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]])

• replacements (list[str])

• rootdir (pathlib.Path)

• types (list[Literal[junifer.datagrabber.base.DataType.VBM_GM]])

• uri (pydantic.networks.HttpUrl)

Validators:

field patterns: dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]] = {'VBM_GM': {'pattern': 'm0wp1{subject}_ses-{session}_T1w.nii.gz', 'space': 'IXI549Space'}}

field replacements: list[str] = ['subject', 'session']

field rootdir: Path = PosixPath('m0wp1')

field types: list[Literal[DataType.VBM_GM]] = [<DataType.VBM_GM: 'VBM_GM'>]

field uri: HttpUrl = 'ria+http://ukb.ds.inm7.de#~cat_m0wp1'

model_post_init(context)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

pydantic model junifer.configs.juseless.datagrabbers.JuselessUCLA

Concrete implementation for Juseless UCLA data fetching.

Implements a DataGrabber to access the UCLA data in Juseless.

Parameters:

datadirPath, optional

The directory where the dataset is stored. (default “/data/project/psychosis_thalamus/data/fmriprep”).

types: list of {``DataType.BOLD``, ``DataType.T1w``, ``DataType.VBM_CSF``, ``DataType.VBM_GM``, ``DataType.VBM_WM``}, optional

The data type(s) to grab.

taskslist of UCLATask, optional

UCLA task sessions. By default, all available task are selected.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Show JSON schema

{
   "title": "JuselessUCLA",
   "description": "Concrete implementation for Juseless UCLA data fetching.\n\nImplements a DataGrabber to access the UCLA data in Juseless.\n\nParameters\n----------\ndatadir : Path, optional\n    The directory where the dataset is stored.\n    (default \"/data/project/psychosis_thalamus/data/fmriprep\").\ntypes: list of {``DataType.BOLD``, ``DataType.T1w``,            ``DataType.VBM_CSF``, ``DataType.VBM_GM``, ``DataType.VBM_WM``},            optional\n    The data type(s) to grab.\ntasks : list of ``UCLATask``, optional\n    UCLA task sessions.\n    By default, all available task are selected.",
   "type": "object",
   "properties": {
      "types": {
         "default": [
            "BOLD",
            "T1w",
            "VBM_CSF",
            "VBM_GM",
            "VBM_WM"
         ],
         "items": {
            "enum": [
               "BOLD",
               "T1w",
               "VBM_CSF",
               "VBM_GM",
               "VBM_WM"
            ],
            "type": "string"
         },
         "title": "Types",
         "type": "array"
      },
      "datadir": {
         "default": "/data/project/psychosis_thalamus/data/fmriprep",
         "format": "path",
         "title": "Datadir",
         "type": "string"
      },
      "patterns": {
         "additionalProperties": {
            "anyOf": [
               {
                  "additionalProperties": {
                     "anyOf": [
                        {
                           "type": "string"
                        },
                        {
                           "additionalProperties": {
                              "type": "string"
                           },
                           "type": "object"
                        },
                        {
                           "items": {
                              "additionalProperties": {
                                 "type": "string"
                              },
                              "type": "object"
                           },
                           "type": "array"
                        }
                     ]
                  },
                  "type": "object"
               },
               {
                  "items": {
                     "additionalProperties": {
                        "type": "string"
                     },
                     "type": "object"
                  },
                  "type": "array"
               }
            ]
         },
         "default": {
            "BOLD": {
               "confounds": {
                  "pattern": "{subject}/func/{subject}_task-{task}_bold_confounds.tsv",
                  "space": "fmriprep"
               },
               "pattern": "{subject}/func/{subject}_task-{task}_bold_space-MNI152NLin2009cAsym_preproc.nii.gz",
               "space": "MNI152NLin2009cAsym"
            },
            "T1w": {
               "pattern": "{subject}/anat/{subject}_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz",
               "space": "MNI152NLin2009cAsym"
            },
            "VBM_CSF": {
               "pattern": "{subject}/anat/{subject}_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz",
               "space": "MNI152NLin2009cAsym"
            },
            "VBM_GM": {
               "pattern": "{subject}/anat/{subject}_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz",
               "space": "MNI152NLin2009cAsym"
            },
            "VBM_WM": {
               "pattern": "{subject}/anat/{subject}_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz",
               "space": "MNI152NLin2009cAsym"
            }
         },
         "title": "Patterns",
         "type": "object"
      },
      "replacements": {
         "default": [
            "subject",
            "task"
         ],
         "items": {
            "type": "string"
         },
         "title": "Replacements",
         "type": "array"
      },
      "confounds_format": {
         "$ref": "#/$defs/ConfoundsFormat",
         "default": "fmriprep"
      },
      "partial_pattern_ok": {
         "default": false,
         "title": "Partial Pattern Ok",
         "type": "boolean"
      },
      "tasks": {
         "default": [
            "rest",
            "bart",
            "bht",
            "pamenc",
            "pamret",
            "scap",
            "taskswitch",
            "stopsignal"
         ],
         "items": {
            "$ref": "#/$defs/UCLATask"
         },
         "title": "Tasks",
         "type": "array"
      }
   },
   "$defs": {
      "ConfoundsFormat": {
         "description": "Accepted confounds format.",
         "enum": [
            "fmriprep",
            "adhoc"
         ],
         "title": "ConfoundsFormat",
         "type": "string"
      },
      "UCLATask": {
         "description": "Accepted UCLA tasks.",
         "enum": [
            "rest",
            "bart",
            "bht",
            "pamenc",
            "pamret",
            "scap",
            "taskswitch",
            "stopsignal"
         ],
         "title": "UCLATask",
         "type": "string"
      }
   }
}

Config:

• use_enum_values: bool = True

Fields:

• confounds_format (junifer.datagrabber.pattern.ConfoundsFormat)

• datadir (pathlib.Path)

• patterns (dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]])

• replacements (list[str])

• tasks (list[junifer.configs.juseless.datagrabbers.ucla.UCLATask])

• types (list[Literal[junifer.datagrabber.base.DataType.BOLD, junifer.datagrabber.base.DataType.T1w, junifer.datagrabber.base.DataType.VBM_CSF, junifer.datagrabber.base.DataType.VBM_GM, junifer.datagrabber.base.DataType.VBM_WM]])

field confounds_format: ConfoundsFormat = ConfoundsFormat.FMRIPrep

field datadir: Path = PosixPath('/data/project/psychosis_thalamus/data/fmriprep')

field patterns: dict[str, dict[str, str | dict[str, str] | list[dict[str, str]]] | list[dict[str, str]]] = {'BOLD': {'confounds': {'pattern': '{subject}/func/{subject}_task-{task}_bold_confounds.tsv', 'space': 'fmriprep'}, 'pattern': '{subject}/func/{subject}_task-{task}_bold_space-MNI152NLin2009cAsym_preproc.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'T1w': {'pattern': '{subject}/anat/{subject}_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_CSF': {'pattern': '{subject}/anat/{subject}_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_GM': {'pattern': '{subject}/anat/{subject}_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz', 'space': 'MNI152NLin2009cAsym'}, 'VBM_WM': {'pattern': '{subject}/anat/{subject}_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz', 'space': 'MNI152NLin2009cAsym'}}

field replacements: list[str] = ['subject', 'task']

field tasks: list[UCLATask] = [UCLATask.REST, UCLATask.BART, UCLATask.BHT, UCLATask.PAMENC, UCLATask.PAMRET, UCLATask.SCAP, UCLATask.TASKSWITCH, UCLATask.STOPSIGNAL]

field types: list[Literal[DataType.BOLD, DataType.T1w, DataType.VBM_CSF, DataType.VBM_GM, DataType.VBM_WM]] = [<DataType.BOLD: 'BOLD'>, <DataType.T1w: 'T1w'>, <DataType.VBM_CSF: 'VBM_CSF'>, <DataType.VBM_GM: 'VBM_GM'>, <DataType.VBM_WM: 'VBM_WM'>]

get_elements()

Implement fetching list of elements in the dataset.

Returns:

elementslist

The list of elements that can be grabbed in the dataset after imposing constraints based on specified tasks.

enum junifer.configs.juseless.datagrabbers.UCLATask(value)

Accepted UCLA tasks.

Member Type:

str

Valid values are as follows:

REST = <UCLATask.REST: 'rest'>

BART = <UCLATask.BART: 'bart'>

BHT = <UCLATask.BHT: 'bht'>

PAMENC = <UCLATask.PAMENC: 'pamenc'>

PAMRET = <UCLATask.PAMRET: 'pamret'>

SCAP = <UCLATask.SCAP: 'scap'>

TASKSWITCH = <UCLATask.TASKSWITCH: 'taskswitch'>

STOPSIGNAL = <UCLATask.STOPSIGNAL: 'stopsignal'>