fix mri-preproc

ohbm · May 18, 2024 · de0a68d · de0a68d
1 parent 634473b
commit de0a68d
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Showing 85 changed files with 618 additions and 396 deletions.
diff --git a/schemas/mri/activities/preprocessing/items/anatomical_image_intensity_correction.jsonld b/schemas/mri/activities/preprocessing/items/anatomical_image_intensity_correction.jsonld
@@ -2,20 +2,16 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "anatomical_image_intensity_correction.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "anatomical image intensity correction"
     },
     "description": "anatomical image intensity correction",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "textarea"
     },
     "question": {
         "en": "1.96 - Specify the type of intensity correction of the anatomical image<div style='font-size: 70%; text-align:left;'><details> <summary> details </summary> <br>Bias field corrections for anatomical MRI</details></div>"
-    },
-    "responseOptions": {
-        "valueType": "xsd:string",
-        "maxLength": 300
     }
 }
diff --git a/schemas/mri/activities/preprocessing/items/bet_manual_edit.jsonld b/schemas/mri/activities/preprocessing/items/bet_manual_edit.jsonld
@@ -2,20 +2,16 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "bet_manual_edit.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "bet manual edit"
     },
     "description": "bet manual edit",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "textarea"
     },
     "question": {
         "en": "1.13 - Describe any eventual manual editing done to the brainmask."
-    },
-    "responseOptions": {
-        "valueType": "xsd:string",
-        "maxLength": 300
     }
 }
diff --git a/schemas/mri/activities/preprocessing/items/bet_method.jsonld b/schemas/mri/activities/preprocessing/items/bet_method.jsonld
@@ -2,12 +2,12 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "bet_method.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "bet method"
     },
     "description": "bet method",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "radio"
     },
@@ -16,8 +16,6 @@
     },
     "responseOptions": {
         "valueType": "xsd:integer",
-        "minValue": 0,
-        "maxValue": 2,
         "choices": [
             {
                 "name": {
@@ -38,6 +36,7 @@
                 "value": 2
             }
         ],
-        "multipleChoice": false
+        "minValue": 0,
+        "maxValue": 2
     }
 }
diff --git a/schemas/mri/activities/preprocessing/items/bet_parameters.jsonld b/schemas/mri/activities/preprocessing/items/bet_parameters.jsonld
@@ -2,20 +2,16 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "bet_parameters.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "bet parameters"
     },
     "description": "bet parameters",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "textarea"
     },
     "question": {
         "en": "1.12 - Parameters used for the brain extraction<div style='font-size: 70%; text-align:left;'><details> <summary> details </summary> <br>For example BET\u2019s fractional intensity threshold</details></div>"
-    },
-    "responseOptions": {
-        "valueType": "xsd:string",
-        "maxLength": 300
     }
 }
diff --git a/schemas/mri/activities/preprocessing/items/bet_software.jsonld b/schemas/mri/activities/preprocessing/items/bet_software.jsonld
@@ -2,17 +2,22 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "bet_software.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "bet software"
     },
     "description": "bet software",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "select"
     },
     "question": {
         "en": "1.9 - Software used for the brain extraction"
     },
-    "responseOptions": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld"
+    "responseOptions": {
+        "valueType": "xsd:integer",
+        "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld",
+        "minValue": 0,
+        "maxValue": 0
+    }
 }
diff --git a/schemas/mri/activities/preprocessing/items/bet_version.jsonld b/schemas/mri/activities/preprocessing/items/bet_version.jsonld
@@ -2,20 +2,16 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "bet_version.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "bet version"
     },
     "description": "bet version",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "textarea"
     },
     "question": {
         "en": "1.10 - Software version used for the brain extraction"
-    },
-    "responseOptions": {
-        "valueType": "xsd:string",
-        "maxLength": 300
     }
 }
diff --git a/schemas/mri/activities/preprocessing/items/denoising_used.jsonld b/schemas/mri/activities/preprocessing/items/denoising_used.jsonld
@@ -2,17 +2,22 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "denoising_used.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "denoising used"
     },
     "description": "denoising used",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "radio"
     },
     "question": {
         "en": "1.99 - Was any kind of denoising performed or were any nuisance covariate included in the subject level model?"
     },
-    "responseOptions": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld"
+    "responseOptions": {
+        "valueType": "xsd:integer",
+        "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/boolean.jsonld",
+        "minValue": 0,
+        "maxValue": 0
+    }
 }
diff --git a/schemas/mri/activities/preprocessing/items/dwi_subject_custom_atlas.jsonld b/schemas/mri/activities/preprocessing/items/dwi_subject_custom_atlas.jsonld
@@ -2,20 +2,16 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "dwi_subject_custom_atlas.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "dwi subject custom atlas"
     },
     "description": "dwi subject custom atlas",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "textarea"
     },
     "question": {
         "en": "1.54 - Diffusion weighted imaging:<br>Specify set of subjects used to create custom atlas"
-    },
-    "responseOptions": {
-        "valueType": "xsd:string",
-        "maxLength": 300
     }
 }
diff --git a/schemas/mri/activities/preprocessing/items/filtering_approach.jsonld b/schemas/mri/activities/preprocessing/items/filtering_approach.jsonld
@@ -2,12 +2,12 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "filtering_approach.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "filtering approach"
     },
     "description": "filtering approach",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "radio"
     },
@@ -16,8 +16,6 @@
     },
     "responseOptions": {
         "valueType": "xsd:integer",
-        "minValue": 0,
-        "maxValue": 1,
         "choices": [
             {
                 "name": {
@@ -32,6 +30,7 @@
                 "value": 1
             }
         ],
-        "multipleChoice": false
+        "minValue": 0,
+        "maxValue": 1
     }
 }
diff --git a/schemas/mri/activities/preprocessing/items/func_anat_coreg_cost_function.jsonld b/schemas/mri/activities/preprocessing/items/func_anat_coreg_cost_function.jsonld
@@ -2,17 +2,22 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "func_anat_coreg_cost_function.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "func anat coreg cost function"
     },
     "description": "func anat coreg cost function",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "radio"
     },
     "question": {
         "en": "1.73 - Similarity metric used for functional - anatomical coregistration<div style='font-size: 70%; text-align:left;'><details> <summary> details </summary> <br>Image similarity metric</details></div>"
     },
-    "responseOptions": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/cost_functions.jsonld"
+    "responseOptions": {
+        "valueType": "xsd:integer",
+        "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/cost_functions.jsonld",
+        "minValue": 0,
+        "maxValue": 0
+    }
 }
diff --git a/schemas/mri/activities/preprocessing/items/func_anat_coreg_dof.jsonld b/schemas/mri/activities/preprocessing/items/func_anat_coreg_dof.jsonld
@@ -2,12 +2,12 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "func_anat_coreg_dof.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "func anat coreg dof"
     },
     "description": "func anat coreg dof",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "float"
     },

diff --git a/schemas/mri/activities/preprocessing/items/func_anat_coreg_interpolation_method.jsonld b/schemas/mri/activities/preprocessing/items/func_anat_coreg_interpolation_method.jsonld
@@ -2,17 +2,22 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "func_anat_coreg_interpolation_method.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "func anat coreg interpolation method"
     },
     "description": "func anat coreg interpolation method",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "select"
     },
     "question": {
         "en": "1.74 - Interpolation method used for the functional - anatomical coregistration"
     },
-    "responseOptions": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/interpolations.jsonld"
+    "responseOptions": {
+        "valueType": "xsd:integer",
+        "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/interpolations.jsonld",
+        "minValue": 0,
+        "maxValue": 0
+    }
 }
diff --git a/schemas/mri/activities/preprocessing/items/func_anat_coreg_method.jsonld b/schemas/mri/activities/preprocessing/items/func_anat_coreg_method.jsonld
@@ -2,20 +2,16 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "func_anat_coreg_method.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "func anat coreg method"
     },
     "description": "func anat coreg method",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "textarea"
     },
     "question": {
         "en": "1.69 - Method used for the functional - anatomical coregistration"
-    },
-    "responseOptions": {
-        "valueType": "xsd:string",
-        "maxLength": 300
     }
 }
diff --git a/schemas/mri/activities/preprocessing/items/func_anat_coreg_software.jsonld b/schemas/mri/activities/preprocessing/items/func_anat_coreg_software.jsonld
@@ -2,17 +2,22 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "func_anat_coreg_software.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "func anat coreg software"
     },
     "description": "func anat coreg software",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "select"
     },
     "question": {
         "en": "1.67 - Software used for the functional - anatomical coregistration"
     },
-    "responseOptions": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld"
+    "responseOptions": {
+        "valueType": "xsd:integer",
+        "choices": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/response_options/mri_softwares.jsonld",
+        "minValue": 0,
+        "maxValue": 0
+    }
 }
diff --git a/schemas/mri/activities/preprocessing/items/func_anat_coreg_source_volume.jsonld b/schemas/mri/activities/preprocessing/items/func_anat_coreg_source_volume.jsonld
@@ -2,20 +2,16 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "func_anat_coreg_source_volume.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "func anat coreg source volume"
     },
     "description": "func anat coreg source volume",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "textarea"
     },
     "question": {
         "en": "1.71 - Source volume used for the functional - anatomical coregistration"
-    },
-    "responseOptions": {
-        "valueType": "xsd:string",
-        "maxLength": 300
     }
 }
diff --git a/schemas/mri/activities/preprocessing/items/func_anat_coreg_target_volume.jsonld b/schemas/mri/activities/preprocessing/items/func_anat_coreg_target_volume.jsonld
@@ -2,20 +2,16 @@
     "@context": "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic",
     "@type": "reproschema:Field",
     "@id": "func_anat_coreg_target_volume.jsonld",
+    "schemaVersion": "1.0.0-rc4",
+    "version": "0.0.1",
     "prefLabel": {
         "en": "func anat coreg target volume"
     },
     "description": "func anat coreg target volume",
-    "schemaVersion": "1.0.0-rc4",
-    "version": "0.0.1",
     "ui": {
         "inputType": "textarea"
     },
     "question": {
         "en": "1.70 - Target volume used for the functional - anatomical coregistration"
-    },
-    "responseOptions": {
-        "valueType": "xsd:string",
-        "maxLength": 300
     }
 }