Merge pull request #115 from brainlife/enh/more_metadata

[ENH] Expand metadata editing capabilities

ui/src/Objects.vue

@@ -285,7 +285,13 @@
                                 >
                             </p>
                             <el-form-item
-                                v-if="['perf/asl', 'perf/m0scan'].includes(so._type) || so._type.startsWith('pet/')"
+                                v-if="
+                                    ['perf/asl', 'perf/m0scan'].includes(so._type) ||
+                                    so._type.startsWith('pet') ||
+                                    so._type.startsWith('func') ||
+                                    so._type.startsWith('fmap') ||
+                                    so._type.startsWith('dwi')
+                                "
                                 label="Relevant Metadata"
                             >
                                 <ModalityForm :ss="so" :ezbids="ezbids" @form-submitted="submitForm" />

ui/src/SeriesPage.vue

@@ -236,7 +236,13 @@
                     </el-form-item>
                     <br />
                     <el-form-item
-                        v-if="['perf/asl', 'perf/m0scan'].includes(ss.type) || ss.type.startsWith('pet/')"
+                        v-if="
+                            ['perf/asl', 'perf/m0scan'].includes(ss.type) ||
+                            ss.type.startsWith('pet') ||
+                            ss.type.startsWith('func') ||
+                            ss.type.startsWith('fmap') ||
+                            ss.type.startsWith('dwi')
+                        "
                         label="Relevant Metadata"
                     >
                         <ModalityForm :ss="ss" :ezbids="ezbids" @form-submitted="submitForm" />

ui/src/assets/schema/rules/sidecars/dwi.yaml

@@ -0,0 +1,20 @@
+---
+# Multipart (split) DWI schemes
+# NOTE: I don't think this can be schemafied, since it depends on owner intent.
+MRIDiffusionMultipart:
+  selectors:
+    - datatype == "dwi"
+    - suffix == "dwi"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    MultipartID: optional
+
+# Other recommended metadata
+MRIDiffusionOtherMetadata:
+  selectors:
+    - datatype == "dwi"
+    - suffix == "dwi"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    PhaseEncodingDirection: recommended
+    TotalReadoutTime: recommended

ui/src/assets/schema/rules/sidecars/fmap.yaml

@@ -0,0 +1,71 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+---
+# Fieldmap data
+MRIFieldmapIntendedFor:
+  selectors:
+    - datatype == "fmap"
+    - match(extension, '\.nii(\.gz)?$')
+  fields:
+    IntendedFor:
+      level: optional
+      description_addendum: |
+        This field is optional, and in case the fieldmaps do not correspond
+        to any particular scans, it does not have to be filled.
+
+MRIFieldmapB0FieldIdentifier:
+  selectors:
+    - datatype == "fmap"
+    - match(extension, '\.nii(\.gz)?$')
+    - '!("IntendedFor" in sidecar)'
+  fields:
+    B0FieldIdentifier: recommended
+
+# Case 1: Phase-difference map and at least one magnitude image
+MRIFieldmapPhaseDifferencePhasediff:
+  selectors:
+    - datatype == "fmap"
+    - suffix == "phasediff"
+    - match(extension, '\.nii(\.gz)?$')
+  fields:
+    EchoTime1: required
+    EchoTime2: required
+
+# Case 2: Two phase maps and two magnitude images
+# NOTE: Need to check for presence of related files.
+# For example, magnitude1 needs EchoTime__fmap only if phase1 file exists,
+# but EchoTime1 if phasediff exists.
+MRIFieldmapTwoPhase:
+  selectors:
+    - datatype == "fmap"
+    - intersects([suffix], ["phase1", "phase2"])
+    - match(extension, '\.nii(\.gz)?$')
+  fields:
+    EchoTime__fmap: required
+
+# Case 3: Direct field mapping
+MRIFieldmapDirectFieldMapping:
+  selectors:
+    - datatype == "fmap"
+    - suffix == "fieldmap"
+    - match(extension, '\.nii(\.gz)?$')
+  fields:
+    Units:
+      level: required
+      description_addendum: |
+        Fieldmaps must be in units of Hertz (`"Hz"`),
+        radians per second (`"rad/s"`), or Tesla (`"T"`).
+
+# Case 4: Multiple phase encoded directions ("pepolar")
+MRIFieldmapPepolar:
+  selectors:
+    - datatype == "fmap"
+    - suffix == "epi"
+    - match(extension, '\.nii(\.gz)?$')
+  fields:
+    PhaseEncodingDirection: required
+    TotalReadoutTime: required

ui/src/assets/schema/rules/sidecars/func.yaml

@@ -0,0 +1,88 @@
+#
+# Groups of related metadata fields
+#
+# Assumptions: never need disjunction of selectors
+# Assumptions: top-to-bottom overrides is sufficient logic
+
+---
+# Task imaging data
+
+# Required fields
+MRIFuncRequired:
+  selectors:
+    - datatype == "func"
+    - suffix == "bold"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    TaskName:
+      level: required
+      description_addendum: |
+        A recommended convention is to name resting state task using labels
+        beginning with `rest`.
+
+MRIFuncRepetitionTime:
+  selectors:
+    - datatype == "func"
+    - suffix == "bold"
+    - '!("VolumeTiming" in sidecar)'
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    RepetitionTime:
+      level: required
+      level_addendum: mutually exclusive with `VolumeTiming`
+
+MRIFuncVolumeTiming:
+  selectors:
+    - datatype == "func"
+    - suffix == "bold"
+    - '!("RepetitionTime" in sidecar)'
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    VolumeTiming:
+      level: required
+      level_addendum: mutually exclusive with `RepetitionTime`
+
+# Timing Parameters
+MRIFuncTimingParameters:
+  selectors:
+    - datatype == "func"
+    - suffix == "bold"
+  fields:
+    NumberOfVolumesDiscardedByScanner: recommended
+    NumberOfVolumesDiscardedByUser: recommended
+    DelayTime: recommended
+    AcquisitionDuration:
+      level: recommended
+      level_addendum: |
+        required for sequences that are described with the `VolumeTiming`
+        field and that do not have the `SliceTiming` field set to allow for
+        accurate calculation of "acquisition time"
+      issue:
+        name: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
+        message: |
+          The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
+    DelayAfterTrigger: recommended
+
+# fMRI task information
+MRIFuncTaskInformation:
+  selectors:
+    - datatype == "func"
+    - suffix == "bold"
+  fields:
+    Instructions:
+      level: recommended
+      description_addendum: |
+        This is especially important in context of resting state recordings and
+        distinguishing between eyes open and eyes closed paradigms.
+    TaskDescription: recommended
+    CogAtlasID: recommended
+    CogPOID: recommended
+
+# Should now be `part-phase_bold.nii`, but still require units
+PhaseSuffixUnits:
+  selectors:
+    - datatype == "func"
+    - suffix == "phase"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    Units: required

ui/src/components/modalityForm.vue

@@ -507,6 +507,9 @@
 <script lang="ts">
 import aslYaml from '../../src/assets/schema/rules/sidecars/asl.yaml';
 import petYaml from '../../src/assets/schema/rules/sidecars/pet.yaml';
+import funcYaml from '../../src/assets/schema/rules/sidecars/func.yaml';
+import dwiYaml from '../../src/assets/schema/rules/sidecars/dwi.yaml';
+import fmapYaml from '../../src/assets/schema/rules/sidecars/fmap.yaml';
 
 import metadata_types from '../../src/assets/schema/rules/sidecars/metadata_types.yaml';
 import { ElMessageBox, ElMessage, useFocus } from 'element-plus';
@@ -654,6 +657,12 @@ export default defineComponent({
                 fileObject = aslYaml;
             } else if (type.startsWith('pet')) {
                 fileObject = petYaml;
+            } else if (type.startsWith('func')) {
+                fileObject = funcYaml;
+            } else if (type.startsWith('dwi')) {
+                fileObject = dwiYaml;
+            } else if (type.startsWith('fmap')) {
+                fileObject = fmapYaml;
             }
             let result = {
                 required: [],
@@ -682,6 +691,10 @@ export default defineComponent({
                     if (type === 'pet/pet' && section.includes('Blood')) {
                         continue;
                     }
+                    //TODO - Need to come back to this and make the underlying code better at accounting for these
+                    if (type.startsWith('func') && ['TaskName', 'VolumeTiming', 'Units'].includes(field)) {
+                        continue;
+                    }
 
                     // get the metadata from the metadata_types.yaml
                     const details = metadata_types[field] || {};
@@ -1125,6 +1138,10 @@ export default defineComponent({
                         // regex to get CASL
                         const regex = /objects.enums.(\w+).value/;
                         const refObject = regex.exec(item['$ref']);
+                        // Spec PED info contains the phrase "Minus" rather than the actual symbol (-). Correct this here
+                        if (refObject[1].endsWith('Minus')) {
+                            refObject[1] = refObject[1].replace('Minus', '-');
+                        }
                         return { value: refObject[1], label: refObject[1] };
                     }
                 }