complete meg

src/bids-cfood/cfood.yml

@@ -65,10 +65,15 @@ metadata:
             role: File
             path: $$${parent}_datafile
             file: ${parent}_datafile  # this is automatically the relative path
+            recordingLabel: $$recording
+            spaceLabel: $$space
+            ProcessedOnDevice: $$proc
+            Split: $$split
           Magnetoencephalography:
             RawData: +$$someFile
             Acquisition_label: $$acq
             RunLabel: $$run
+            Task: $$task
   - !defmacro
     name: EEGDataFile
     params:
@@ -401,6 +406,16 @@ project_level:
                         parent: "PhysiologicalRecording"
                       - suffix: "stim"
                         parent: "ContinuousRecording"
+                      - suffix: "channels"
+                        parent: "ChannelFile"
+                      - suffix: "coordsystem"
+                        parent: "CoordinateSystemFile"
+                      - suffix: "electrodes"
+                        parent: "ElectrodeFile"
+                      - suffix: "photo"
+                        parent: "PhotoFile"
+                      - suffix: "headshape"
+                        parent: "HeadshapeFile"
             eeg:
               type: BIDSEEGDirectory
               match: ^(?P<datatype>eeg)$
@@ -427,6 +442,8 @@ project_level:
                         parent: "ContinuousRecording"
                       - suffix: "channels"
                         parent: "ChannelFile"
+                      - suffix: "coordsystem"
+                        parent: "CoordinateSystemFile"
                       - suffix: "electrodes"
                         parent: "ElectrodeFile"
                       - suffix: "photo"

src/bids-cfood/identifiables.yml

@@ -25,6 +25,7 @@ Electroencephalography:
   - is_referenced_by: [Session]
 Magnetoencephalography:
   - Acquisition_label
+  - Task
   - RunLabel
   - is_referenced_by: [Session]
 Subject:

src/bids-cfood/model.yml

@@ -143,14 +143,6 @@ T1WeightedImage:
     description:  In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weighting in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, TurboFLASH or MP-RAGE). https://bids-specification.readthedocs.io/en/stable/glossary.html#objects.suffixes.T1w
     inherit_from_suggested:
         - RawData
-MagnetoencephalographyDataFile:
-    inherit_from_suggested:
-        - RawData
-    description:  Magnetoencephalography https://bids-specification.readthedocs.io/en/stable/glossary.html#meg-datatypes
-MEGSensorCoilPositions:
-    inherit_from_suggested:
-        - RawData
-    description:  "Another manufacturer-specific detail pertains to the KIT/Yokogawa/Ricoh system, which saves the MEG sensor coil positions in a separate file with two possible filename extensions (.sqd, .mrk). For these files, the markers suffix MUST be used. For example: sub-01_task-nback_markers.sqd  https://bids-specification.readthedocs.io/en/stable/glossary.html#markers-suffixes"
 PhaseMap1:
     inherit_from_suggested:
         - RawData
@@ -205,6 +197,47 @@ AnatomyImaging:
 Magnetoencephalography:
     inherit_from_suggested:
         - DataAcquisition
+
+    recommended_properties:
+        CoordinateSystemFile:
+        MEGSCANSFile:
+            datatype: TEXT
+            description: tsv file describing multiple MEG recording (e.g. runs) (optional) TODO unused
+        ChannelFile:
+        TimingInformation:
+        SQDFile:
+            description: sqd marker file for KIT/Ricoh/Yokogava TODO unused
+            datatype: TEXT
+        MRKFile:
+            description: mrk marker file for KIT/Ricoh/Yokogava TODO unused
+            datatype: TEXT
+        MagnetoencephalographyDataFile:
+            inherit_from_suggested:
+                - RawData
+            description:  Magnetoencephalography https://bids-specification.readthedocs.io/en/stable/glossary.html#meg-datatypes
+            recommended_properties:
+              Split:
+                datatype: TEXT
+                description: "In the case of long data recordings that exceed a file size of 2Gb, .fif files are conventionally split into multiple parts. Each of these files has an internal pointer to the next file. This is important when renaming these split recordings to the BIDS convention.
+
+Instead of a simple renaming, files should be read in and saved under their new names with dedicated tools like MNE-Python, which will ensure that not only the file names, but also the internal file pointers, will be updated.
+
+It is RECOMMENDED that .fif files with multiple parts use the split-<index> entity to indicate each part. If there are multiple parts of a recording and the optional scans.tsv is provided, all files MUST be listed separately in scans.tsv and the entries for the acq_time column in scans.tsv MUST all be identical, as described in Scans file. https://bids-specification.readthedocs.io/en/stable/appendices/entities.html#split"
+              ProcessedOnDevice:
+                datatype: TEXT
+                description: "The proc label is analogous to rec for MR and denotes a variant of a file that was a result of particular processing performed on the device.
+
+This is useful for files produced in particular by Elekta's MaxFilter (for example, sss, tsss, trans, quat or mc), which some installations impose to be run on raw data because of active shielding software corrections before the MEG data can actually be exploited. https://bids-specification.readthedocs.io/en/stable/appendices/entities.html#proc"
+
+
+        HeadshapeFile:
+            inherit_from_suggested:
+                - RawData
+            description:  The 3-D locations of points that describe the head shape and/or electrode locations can be digitized and stored in separate files. https://bids-specification.readthedocs.io/en/stable/glossary.html#headshape-suffixes
+        MEGSensorCoilPositions:
+            inherit_from_suggested:
+                - RawData
+            description:  "Another manufacturer-specific detail pertains to the KIT/Yokogawa/Ricoh system, which saves the MEG sensor coil positions in a separate file with two possible filename extensions (.sqd, .mrk). For these files, the markers suffix MUST be used. For example: sub-01_task-nback_markers.sqd  https://bids-specification.readthedocs.io/en/stable/glossary.html#markers-suffixes"
 Electroencephalography:
     description: eeg recordings
     inherit_from_suggested: