Added NWB file example

README.md

@@ -237,6 +237,7 @@ bids-examples (in alphabetical order).
 | eeg_ds000117           | @robertoostenveld | Multimodal (fMRI, MEG, EEG) stripped down to EEG with MRI anatomical scan and electrode coordinates. EEGLAB data format (.set, .fdt) | anat                  |     | eeg |      |          | https://openneuro.org/datasets/ds000117/                       |
 | eeg_rest_fmri          | @cpernet          | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk)                                                   | anat, dwi, func       |     | eeg |      |          |                                                                |
 | ieeg_epilepsy          | @ftadel           | multiple sessions, tutorial                                                                                                          | anat                  |     |     | ieeg |          | https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids |
+| ieeg_epilepsyNWB       | @TheChymera       | multiple sessions, tutorial — derivative dataset of `ieeg_epilepsy` showcasing the NWB file format alternative                       | anat                  |     |     | ieeg |          | https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids |
 | ieeg_epilepsy_ecog     | @ftadel           | multiple sessions, tutorial                                                                                                          | anat                  |     |     | ieeg |          | https://neuroimage.usc.edu/bst/getupdate.php?s=sample_ecog     |
 | ieeg_visual_multimodal | @irisgroen        |                                                                                                                                      | anat, fmap, func      |     |     | ieeg |          |                                                                |
 | genetics_ukbb          | @cpernet          | multiple tasks, T1w, DTI, BOLD, genetic info                                                                                         | anat, dwi, func, fmap |     |     |      | genetics |                                                                |

ieeg_epilepsy/README

@@ -33,6 +33,7 @@ The acquisition methodology is described in the following articles:
 License
 =======
 
-This tutorial dataset (EEG and MRI data) remains property of the Grenoble University Hospital, France. 
-Its use and transfer outside the ImaGIN tutorial, e.g. for research purposes, is prohibited without written consent. 
-For questions, please contact Olivier David, PhD ([email protected]).	
+This tutorial dataset (EEG and MRI data) remains property of the Grenoble University Hospital, France.
+Its use and transfer outside the ImaGIN tutorial, e.g. for research purposes, is prohibited without written consent.
+For questions, please contact Olivier David, PhD ([email protected]).
+The metadata and filename stubs shared in this repository can be used, transferred, and derived, without explicit permission.

ieeg_epilepsyNWB/CHANGES

@@ -0,0 +1,7 @@
+Release history for this Brainstorm/ImaGIN epileptogenicity tutorial dataset.
+
+1.0.1 2022-07-04
+  - Updated to follow new BIDS rules
+
+1.0.0 2018-11-30
+  - Initial release

ieeg_epilepsyNWB/README.md

@@ -0,0 +1,56 @@
+# Dataset Description
+
+This is a copy of the `ieeg_epilepsy` dataset which is part of the `bids_examples` collection.
+Fies with the extension `.eeg` are replaced with `.nwb` files with an empty data matrix and a subject field definition.
+The `ieeg_epilepsy` was chosen for duplication as it was the smallest dataset using the `ieeg` modality.
+
+```python
+import os
+from uuid import uuid4
+from datetime import datetime, timezone
+from dateutil.tz import tzlocal, tzutc
+import pynwb
+from dandi.pynwb_utils import make_nwb_file, metadata_nwb_file_fields
+
+def simple1_nwb_metadata():
+    # very simple assignment with the same values as the key with 1 as suffix
+    metadata = {f: f"{f}1" for f in metadata_nwb_file_fields}
+    metadata["identifier"] = uuid4().hex
+    # subject_fields
+
+    # tune specific ones:
+    # Needs an explicit time zone since otherwise pynwb would add one
+    # But then comparison breaks anyways any ways yoh have tried to set it
+    # for datetime.now.  Taking example from pynwb tests
+    metadata["session_start_time"] = datetime(2017, 4, 15, 12, tzinfo=tzutc())
+    metadata["keywords"] = ["keyword1", "keyword 2"]
+    # since NWB 2.1.0 some fields values become "arrays" which are
+    # then reloaded as tuples, so we force them being tuples here
+    # See e.g. https://github.com/NeurodataWithoutBorders/pynwb/issues/1091
+    for f in "related_publications", "experimenter":
+        metadata[f] = (metadata[f],)
+    return metadata
+
+for i in os.listdir("."):
+    if i.endswith("nwb"):
+        b = simple1_nwb_metadata()
+        a = make_nwb_file(
+            i+"1",
+            subject=pynwb.file.Subject(
+                subject_id="01",
+                date_of_birth=datetime(2016, 12, 1, tzinfo=tzutc()),
+                sex="U",
+                species="Mus musculus",
+            ),
+            **b,
+        )
+        print(a)
+```
+
+
+# Parent Dataset License
+
+This tutorial dataset (EEG and MRI data) remains property of the Grenoble University Hospital, France.
+Its use and transfer outside the ImaGIN tutorial, e.g. for research purposes, is prohibited without written consent.
+For questions, please contact Olivier David, PhD ([email protected]).
+The metadata and filename stubs shared in this repository can be used, transferred, and derived, without explicit permission.

ieeg_epilepsyNWB/dataset_description.json

@@ -0,0 +1,20 @@
+{
+    "Name": "Brainstorm epileptogenicity tutorial",
+    "BIDSVersion": "1.7.0",
+    "License": "This tutorial dataset (EEG and MRI data) remains property of the Grenoble University Hospital, France. Its use and transfer outside the ImaGIN tutorial, e.g. for research purposes, is prohibited without written consent. For questions, please contact Olivier David, PhD ([email protected]).",
+	 "Authors": [
+	  "Olivier David", 
+	  "Thomas Blauwblomme", 
+	  "Anne-Sophie Job", 
+	  "Stephan Chabardès", 
+	  "Dominique Hoffmann",
+	  "Lorella Minotti", 
+	  "Philippe Kahane"
+	 ],
+    "ReferencesAndLinks": [
+        "David O, Blauwblomme T, Job AS, Chabardès S, Hoffmann D, Minotti L, Kahane P, Imaging the seizure onset zone with stereo-electroencephalography, Brain. 2011 Oct;134(10):2898-911",
+        "Lamarche F, Job AS, Deman P, Bhattacharjee M, Hoffmann D, Gallazzini-Crépin C, Bouvard S, Minotti L, Kahane P, David O, Correlation of FDG-PET hypometabolism and SEEG epileptogenicity mapping in patients with drug-resistant focal epilepsy, Epilepsia. 2016 Dec; 57(12):2045–2055",
+        "https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity", 
+        "https://f-tract.eu/tutorials/"
+    ]
+}

ieeg_epilepsyNWB/participants.json

@@ -0,0 +1,15 @@
+{
+    "age": {
+        "LongName": "age",
+        "Description": "age of the participant",
+        "Units": "years"
+    },
+    "sex": {
+        "LongName": "sex",
+        "Description": "sex of the participant",
+        "Levels": {
+            "m": "male",
+            "f": "female"
+        }
+    }
+}

ieeg_epilepsyNWB/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	age	sex
+sub-01	XX	m

ieeg_epilepsyNWB/sub-01/ses-postimp/ieeg/sub-01_ses-postimp_space-IXI549Space_coordsystem.json

@@ -0,0 +1,7 @@
+{
+    "iEEGCoordinateSystem": "IXI549Space",
+    "iEEGCoordinateUnits": "mm",
+    "iEEGCoordinateProcessingDescription": "SEEG contacts manually placed with IntrAnat on the post-implantation T1w MRI, registered on the pre-implantation T1w, and normalized to IXI549Space with SPM12",
+    "iEEGCoordinateProcessingReference": "Deman, P., Bhattacharjee, M., Tadel, F., Job, A. S., Rivière, D., Cointepas, Y., Kahane, P., … David, O. (2018). IntrAnat Electrodes: A Free Database and Visualization Software for Intracranial Electroencephalographic Data Processed for Case and Group Studies. Frontiers in neuroinformatics, 12, 40. doi:10.3389/fninf.2018.00040",
+    "IntendedFor": "sub-01/ses-postimp/anat/sub-01_ses-postimp_T1w.nii.gz"
+}

ieeg_epilepsyNWB/sub-01/ses-postimp/ieeg/sub-01_ses-postimp_space-IXI549Space_electrodes.tsv

@@ -0,0 +1,125 @@
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ieeg_epilepsyNWB/sub-01/ses-postimp/ieeg/sub-01_ses-postimp_space-ScanRAS_coordsystem.json

@@ -0,0 +1,8 @@
+{
+    "iEEGCoordinateSystem": "ScanRAS",
+    "iEEGCoordinateUnits": "mm",
+    "iEEGCoordinateSystemDescription": "Scanner-based RAS coordinates of the post-implantation T1 MRI",
+    "iEEGCoordinateProcessingDescription": "SEEG contacts manually placed with IntrAnat on the post-implantation T1w MRI, which was registered on the pre-implantation T1w",
+    "iEEGCoordinateProcessingReference": "Deman, P., Bhattacharjee, M., Tadel, F., Job, A. S., Rivière, D., Cointepas, Y., Kahane, P., … David, O. (2018). IntrAnat Electrodes: A Free Database and Visualization Software for Intracranial Electroencephalographic Data Processed for Case and Group Studies. Frontiers in neuroinformatics, 12, 40. doi:10.3389/fninf.2018.00040",
+    "IntendedFor": "sub-01/ses-postimp/anat/sub-01_ses-postimp_T1w.nii.gz"
+}