Merge pull request #1567 from mguaypaq/mgp/allow-desc-in-segmentations

[FIX] Re-align the text and the schema for filenames in derivatives

Author: effigies

src/derivatives/common-data-types.md

@@ -180,8 +180,9 @@ Template:
 ```Text
 <pipeline_name>/
     sub-<label>/
-        <datatype>/
-            <source_entities>[_space-<space>][_desc-<label>]_<suffix>.<extension>
+        [ses-<label>/]
+            <datatype>/
+                <source_entities>[_space-<space>][_desc-<label>]_<suffix>.<extension>
 ```
 
 Data is considered to be *preprocessed* or *cleaned* if the data type of the input,

src/derivatives/imaging.md

@@ -10,8 +10,9 @@ Template:
 ```Text
 <pipeline_name>/
     sub-<label>/
-        <datatype>/
-            <source_entities>[_space-<space>][_res-<label>][_den-<label>][_desc-<label>]_<suffix>.<extension>
+        [ses-<label>/]
+            <datatype>/
+                <source_entities>[_space-<space>][_res-<label>][_den-<label>][_desc-<label>]_<suffix>.<extension>
 ```
 
 Volumetric preprocessing does not modify the number of dimensions, and so
@@ -147,8 +148,10 @@ Template:
 ```Text
 <pipeline_name>/
     sub-<label>/
-        anat|func|dwi/
-            <source_entities>[_space-<space>][_res-<label>][_den-<label>][_label-<label>][_desc-<label>]_mask.nii.gz
+        [ses-<label>/]
+            anat|func|dwi/
+                <source_entities>[_space-<space>][_res-<label>][_label-<label>][_desc-<label>]_mask.json
+                <source_entities>[_space-<space>][_res-<label>][_label-<label>][_desc-<label>]_mask.nii[.gz]
 ```
 
 A binary (1 - inside, 0 - outside) mask in the space defined by the [`space` entity](../appendices/entities.md#space).
@@ -264,8 +267,11 @@ Template:
 ```Text
 <pipeline_name>/
     sub-<label>/
-        anat|func|dwi/
-            <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.nii.gz
+        [ses-<label>/]
+            anat|func|dwi/
+                <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_desc-<label>]_dseg.json
+                <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_desc-<label>]_dseg.nii[.gz]
+                <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_desc-<label>]_dseg.tsv
 ```
 
 Example:
@@ -328,8 +334,10 @@ Template:
 ```Text
 <pipeline_name>/
     sub-<label>/
-        func|anat|dwi/
-            <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_label-<label>]_probseg.nii.gz
+        [ses-<label>/]
+            func|anat|dwi/
+                <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_label-<label>][_desc-<label>]_probseg.json
+                <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_label-<label>][_desc-<label>]_probseg.nii[.gz]
 ```
 
 Example:
@@ -402,8 +410,12 @@ Template:
 ```Text
 <pipeline_name>/
     sub-<label>/
-        anat/
-            <source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
+        [ses-<label>/]
+            anat/
+                <source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_desc-<label>]_dseg.json
+                <source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_den-<label>][_desc-<label>]_dseg.label.gii
+                <source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_desc-<label>]_dseg.dlabel.nii
+                <source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_desc-<label>]_dseg.tsv
 ```
 
 The [`hemi-<label>`](../appendices/entities.md#hemi) entity is REQUIRED for GIFTI files storing information about

src/schema/rules/files/deriv/imaging.yaml

@@ -62,7 +62,6 @@ anat_parametric_mask:
     $ref: rules.files.raw.anat.parametric.entities
     space: optional
     resolution: optional
-    density: optional
     label: optional
     description: optional
 
@@ -76,7 +75,6 @@ anat_nonparametric_mask:
     $ref: rules.files.raw.anat.nonparametric.entities
     space: optional
     resolution: optional
-    density: optional
     label: optional
     description: optional
 
@@ -86,11 +84,14 @@ dwi_mask:
   $ref: rules.files.raw.dwi.dwi
   suffixes:
     - mask
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
   entities:
     $ref: rules.files.raw.dwi.dwi.entities
     space: optional
     resolution: optional
-    density: optional
     label: optional
     description: optional
 
@@ -104,7 +105,6 @@ func_mask:
     $ref: rules.files.raw.func.func.entities
     space: optional
     resolution: optional
-    density: optional
     label: optional
     description: optional
 
@@ -117,8 +117,8 @@ anat_parametric_discrete_segmentation:
   entities:
     $ref: rules.files.raw.anat.parametric.entities
     space: optional
+    segmentation: optional
     resolution: optional
-    density: optional
     description: optional
   extensions:
     - .nii.gz
@@ -135,8 +135,8 @@ anat_nonparametric_discrete_segmentation:
   entities:
     $ref: rules.files.raw.anat.nonparametric.entities
     space: optional
+    segmentation: optional
     resolution: optional
-    density: optional
     description: optional
   extensions:
     - .nii.gz
@@ -153,9 +153,14 @@ func_discrete_segmentation:
   entities:
     $ref: rules.files.raw.func.func.entities
     space: optional
+    segmentation: optional
     resolution: optional
-    density: optional
     description: optional
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+    - .tsv
 
 dwi_discrete_segmentation:
   selectors:
@@ -167,8 +172,12 @@ dwi_discrete_segmentation:
     $ref: rules.files.raw.dwi.dwi.entities
     space: optional
     resolution: optional
-    density: optional
     description: optional
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+    - .tsv
 
 anat_parametric_probabilistic_segmentation:
   selectors:
@@ -179,8 +188,8 @@ anat_parametric_probabilistic_segmentation:
   entities:
     $ref: rules.files.raw.anat.parametric.entities
     space: optional
+    segmentation: optional
     resolution: optional
-    density: optional
     label: optional
     description: optional
 
@@ -193,8 +202,8 @@ anat_nonparametric_probabilistic_segmentation:
   entities:
     $ref: rules.files.raw.anat.nonparametric.entities
     space: optional
+    segmentation: optional
     resolution: optional
-    density: optional
     label: optional
     description: optional
 
@@ -207,8 +216,8 @@ func_probabilistic_segmentation:
   entities:
     $ref: rules.files.raw.func.func.entities
     space: optional
+    segmentation: optional
     resolution: optional
-    density: optional
     label: optional
     description: optional
 
@@ -221,12 +230,16 @@ dwi_probabilistic_segmentation:
   entities:
     $ref: rules.files.raw.dwi.dwi.entities
     space: optional
+    segmentation: optional
     resolution: optional
-    density: optional
     label: optional
     description: optional
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
 
-anat_parametic_discrete_surface:
+anat_parametric_discrete_surface:
   selectors:
     - dataset.dataset_description.DatasetType == 'derivative'
   $ref: rules.files.raw.anat.parametric
@@ -241,11 +254,12 @@ anat_parametic_discrete_surface:
     $ref: rules.files.raw.anat.parametric.entities
     hemisphere: optional
     space: optional
+    segmentation: optional
     resolution: optional
     density: optional
     description: optional
 
-anat_nonparametic_discrete_surface:
+anat_nonparametric_discrete_surface:
   selectors:
     - dataset.dataset_description.DatasetType == 'derivative'
   $ref: rules.files.raw.anat.nonparametric
@@ -260,6 +274,7 @@ anat_nonparametic_discrete_surface:
     $ref: rules.files.raw.anat.nonparametric.entities
     hemisphere: optional
     space: optional
+    segmentation: optional
     resolution: optional
     density: optional
     description: optional