MED example dataset (no data, only headers) #469

MEDFormat · 2024-10-17T17:42:40Z

relates to bids-standard/bids-specification#1956

Remi-Gau · 2024-10-18T10:55:21Z

@MEDFormat you will have to rename the folders to comply with the BIDS data strcuture.

MEDFormat · 2024-10-18T11:00:49Z

What does that mean? MED & MEF (currently accepted by BIDS) require certain naming conventions. Cheers, Matt Matt Stead ***@***.***

…

On Oct 18, 2024, at 4:55 AM, Remi Gau ***@***.***> wrote: @MEDFormat <https://github.com/MEDFormat> you will have to rename the folders to comply with the BIDS data strcuture. — Reply to this email directly, view it on GitHub <#469 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ATNKTHRSZ6SWWSZ7RBFUJJ3Z4DSLBAVCNFSM6AAAAABQEIQVVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRSGE4TENBZGQ>. You are receiving this because you were mentioned.

Remi-Gau · 2024-10-18T11:35:47Z

please check any of the other iEEG datasets in this repo and see how the files are named and try top match this.

for example

tree ../examples/ieeg_epilepsy 
../examples/ieeg_epilepsy
├── CHANGES
├── dataset_description.json
├── derivatives
├── participants.json
├── participants.tsv
├── README
└── sub-01
    ├── ses-postimp
    │   ├── anat
    │   │   └── sub-01_ses-postimp_T1w.nii.gz
    │   ├── ieeg
    │   │   ├── sub-01_ses-postimp_space-IXI549Space_coordsystem.json
    │   │   ├── sub-01_ses-postimp_space-IXI549Space_electrodes.tsv
    │   │   ├── sub-01_ses-postimp_space-ScanRAS_coordsystem.json
    │   │   ├── sub-01_ses-postimp_space-ScanRAS_electrodes.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_channels.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_events.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_ieeg.eeg
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_ieeg.json
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_ieeg.vhdr
    │   │   ├── sub-01_ses-postimp_task-seizure_run-01_ieeg.vmrk
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_channels.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_events.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_ieeg.eeg
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_ieeg.json
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_ieeg.vhdr
    │   │   ├── sub-01_ses-postimp_task-seizure_run-02_ieeg.vmrk
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_channels.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_events.tsv
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_ieeg.eeg
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_ieeg.json
    │   │   ├── sub-01_ses-postimp_task-seizure_run-03_ieeg.vhdr
    │   │   └── sub-01_ses-postimp_task-seizure_run-03_ieeg.vmrk
    │   └── sub-01_ses-postimp_scans.tsv
    └── ses-preimp
        ├── anat
        │   ├── sub-01_ses-preimp_T1w.json
        │   └── sub-01_ses-preimp_T1w.nii.gz
        └── sub-01_ses-preimp_scans.tsv

Given that MED has files listed under a folder I think you may have to follow what is done with MEG for meg.ds

tree ../examples/ds000246 
../examples/ds000246
├── CHANGES
├── dataset_description.json
├── participants.json
├── participants.tsv
├── README
├── sub-0001
│   ├── anat
│   │   └── sub-0001_T1w.nii.gz
│   ├── meg
│   │   ├── sub-0001_acq-LPA_photo.jpg
│   │   ├── sub-0001_acq-NAS_photo.jpg
│   │   ├── sub-0001_acq-RPA_photo.jpg
│   │   ├── sub-0001_coordsystem.json
│   │   ├── sub-0001_headshape.pos
│   │   ├── sub-0001_task-AEF_run-01_channels.tsv
│   │   ├── sub-0001_task-AEF_run-01_meg.ds
│   │   │   ├── BadChannels
│   │   │   ├── ChannelGroupSet.cfg
│   │   │   ├── ClassFile.cls
│   │   │   ├── MarkerFile.mrk
│   │   │   ├── sub-0001_task-AEF_run-01_meg.acq
│   │   │   ├── sub-0001_task-AEF_run-01_meg.eeg
│   │   │   ├── sub-0001_task-AEF_run-01_meg.hc
│   │   │   ├── sub-0001_task-AEF_run-01_meg.hist
│   │   │   ├── sub-0001_task-AEF_run-01_meg.infods
│   │   │   ├── sub-0001_task-AEF_run-01_meg.meg4
│   │   │   └── sub-0001_task-AEF_run-01_meg.res4
│   │   ├── sub-0001_task-AEF_run-01_meg.json
│   │   ├── sub-0001_task-AEF_run-02_channels.tsv
│   │   ├── sub-0001_task-AEF_run-02_meg.ds
│   │   │   ├── BadChannels
│   │   │   ├── ChannelGroupSet.cfg
│   │   │   ├── ClassFile.cls
│   │   │   ├── MarkerFile.mrk
│   │   │   ├── sub-0001_task-AEF_run-02_meg.acq
│   │   │   ├── sub-0001_task-AEF_run-02_meg.eeg
│   │   │   ├── sub-0001_task-AEF_run-02_meg.hc
│   │   │   ├── sub-0001_task-AEF_run-02_meg.hist
│   │   │   ├── sub-0001_task-AEF_run-02_meg.infods
│   │   │   ├── sub-0001_task-AEF_run-02_meg.meg4
│   │   │   ├── sub-0001_task-AEF_run-02_meg.newds
│   │   │   └── sub-0001_task-AEF_run-02_meg.res4
│   │   └── sub-0001_task-AEF_run-02_meg.json
│   └── sub-0001_scans.tsv
└── sub-emptyroom
    ├── meg
    │   ├── sub-emptyroom_task-noise_run-01_channels.tsv
    │   ├── sub-emptyroom_task-noise_run-01_meg.ds
    │   │   ├── BadChannels
    │   │   ├── ClassFile.cls
    │   │   ├── default.de
    │   │   ├── params.dsc
    │   │   ├── processing.cfg
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.acq
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.hc
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.hist
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.infods
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.meg4
    │   │   ├── sub-emptyroom_task-noise_run-01_meg.newds
    │   │   └── sub-emptyroom_task-noise_run-01_meg.res4
    │   └── sub-emptyroom_task-noise_run-01_meg.json
    └── sub-emptyroom_scans.tsv

MEDFormat · 2024-10-18T11:57:44Z

Can you point me to the MEF 3.0 example? I cannot find it, but MED will be almost identical.

MEDFormat · 2024-10-18T12:52:22Z

Contents: Here is a minimal MED tree with all possible file types: Global session records (data & indices) Segmented session records (data & indices) One time series channel (“ts_0001”) One video channel (“vid_0001”) Channel-level records (data & indices) Segment-level records (data & indices) Time series data (data & indices) Time series metadata Video data (data & indices) Video metadata Tree: test.medd ├── test.rdat ├── test.recd │ ├── test_s0001.rdat │ └── test_s0001.ridx ├── test.ridx ├── ts_0001.ticd │ ├── ts_0001.rdat │ ├── ts_0001.ridx │ └── ts_0001_s0001.tisd │ ├── ts_0001_s0001.rdat │ ├── ts_0001_s0001.ridx │ ├── ts_0001_s0001.tdat │ ├── ts_0001_s0001.tidx │ └── ts_0001_s0001.tmet └── vid_0001.ticd ├── vid_0001.rdat ├── vid_0001.ridx └── vid_0001_s0001.tisd ├── vid_0001_s0001.rdat ├── vid_0001_s0001.ridx ├── vid_0001_s0001.tidx ├── vid_0001_s0001.tmet └── vid_0001_s0001_n0001.mp4 Descriptions: test.medd: “test” session directory test.medd/test.rdat session record data (unsegmented) test.medd/test..ridx session record indices (unsegmented) test.medd/test.recd: “test” segmented session record directory test.medd/test.recd/test_s0001.rdat segment 1 session record data test.medd/test.recd/test_s0001.ridx segment 1 session record indices test.medd/ts_0001.ticd: “ts_0001” time series channel directory test.medd/ts_0001.rdat: channel-level record data test.medd/ts_0001.ridx: channel-level record indices test.medd/ts_0001_s0001 segment 1 directory test.medd/ts_0001_s0001.tisd/ts_0001_s0001.rdat: segment-level record data test.medd/ts_0001_s0001.tisd/ts_0001_s0001.ridx: segment-level record indices test.medd/ts_0001_s0001.tisd/ts_0001_s0001.tdat: time series data test.medd/ts_0001_s0001.tisd/ts_0001_s0001.tidx: time series indices test.medd/ts_0001_s0001.tisd/ts_0001_s0001.tmet: time series metadata test.medd/vid_0001.vicd: “vid_0001” video channel directory test.medd/vid_0001.rdat: channel-level record data test.medd/vid_0001.ridx: channel-level record indices test.medd/vid_0001_s0001 segment 1 directory test.medd/vid_0001_s0001.tisd/vid_0001_s0001.rdat: segment-level record data test.medd/vid_0001_s0001.tisd/vid_0001_s0001.ridx: segment-level record indices test.medd/vid_0001_s0001.tisd/vid_0001_s0001.vidx: video indices test.medd/vis_0001_s0001.tisd/vid_0001_s0001.vidx: video metadata test.medd/vid_0001_s0001.tisd/vid_0001_s0001_n0001.mp4: video data file 1 (mp4 format in this example) How can I put this information into BIDS example? Cheers, Matt Matt Stead ***@***.***

…

On Oct 18, 2024, at 5:00 AM, Contact MFO ***@***.***> wrote: What does that mean? MED & MEF (currently accepted by BIDS) require certain naming conventions. Cheers, Matt <MFO-Logo-GIF-small.gif> Matt Stead ***@***.*** > On Oct 18, 2024, at 4:55 AM, Remi Gau ***@***.***> wrote: > > > @MEDFormat <https://github.com/MEDFormat> you will have to rename the folders to comply with the BIDS data strcuture. > > — > Reply to this email directly, view it on GitHub <#469 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ATNKTHRSZ6SWWSZ7RBFUJJ3Z4DSLBAVCNFSM6AAAAABQEIQVVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRSGE4TENBZGQ>. > You are receiving this because you were mentioned. >

MEDFormat · 2024-10-18T12:59:40Z

Copy paste error above:
"vid_0001_s0001.vidx" video metadata
should have been:
"vid_0001_s0001.vmet" video metadata

Remi-Gau · 2024-10-18T13:08:19Z

Can you point me to the MEF 3.0 example?

AFAICT we do not have one

MEDFormat · 2024-10-18T13:12:04Z

Did you happen to see my last post? If not, here is the MED tree (almost identical to MEF3 tree): test.medd ├── test.rdat ├── test.recd │ ├── test_s0001.rdat │ └── test_s0001.ridx ├── test.ridx ├── ts_0001.ticd │ ├── ts_0001.rdat │ ├── ts_0001.ridx │ └── ts_0001_s0001.tisd │ ├── ts_0001_s0001.rdat │ ├── ts_0001_s0001.ridx │ ├── ts_0001_s0001.tdat │ ├── ts_0001_s0001.vidx │ └── ts_0001_s0001.vmet └── vid_0001.ticd ├── vid_0001.rdat ├── vid_0001.ridx └── vid_0001_s0001.tisd ├── vid_0001_s0001.rdat ├── vid_0001_s0001.ridx ├── vid_0001_s0001.vidx ├── vid_0001_s0001.vmet └── vid_0001_s0001_n0001.mp4 Cheers, Matt Matt Stead ***@***.***

…

On Oct 18, 2024, at 7:08 AM, Remi Gau ***@***.***> wrote: Can you point me to the MEF 3.0 example? AFAICT we do not have one — Reply to this email directly, view it on GitHub <#469 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ATNKTHSTF7BWIY5YIZPH2L3Z4EB5VAVCNFSM6AAAAABQEIQVVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRSGQ2DAMRYGQ>. You are receiving this because you were mentioned.

MEDFormat · 2024-10-18T13:16:13Z

NOTE: made this by hand - last tree had a couple of extension mistakes, apologies. This one is correct. Did you happen to see my last post? If not, here is the MED tree (almost identical to MEF3 tree): test.medd ├── test.rdat ├── test.recd │ ├── test_s0001.rdat │ └── test_s0001.ridx ├── test.ridx ├── ts_0001.ticd │ ├── ts_0001.rdat │ ├── ts_0001.ridx │ └── ts_0001_s0001.tisd │ ├── ts_0001_s0001.rdat │ ├── ts_0001_s0001.ridx │ ├── ts_0001_s0001.tdat │ ├── ts_0001_s0001.tidx │ └── ts_0001_s0001.tmet └── vid_0001.vicd ├── vid_0001.rdat ├── vid_0001.ridx └── vid_0001_s0001.visd ├── vid_0001_s0001.rdat ├── vid_0001_s0001.ridx ├── vid_0001_s0001.vidx ├── vid_0001_s0001.vmet └── vid_0001_s0001_n0001.mp4 Cheers, Matt Matt Stead ***@***.***

…

On Oct 18, 2024, at 7:11 AM, Contact MFO ***@***.***> wrote: Did you happen to see my last post? If not, here is the MED tree (almost identical to MEF3 tree): test.medd ├── test.rdat ├── test.recd │ ├── test_s0001.rdat │ └── test_s0001.ridx ├── test.ridx ├── ts_0001.ticd │ ├── ts_0001.rdat │ ├── ts_0001.ridx │ └── ts_0001_s0001.tisd │ ├── ts_0001_s0001.rdat │ ├── ts_0001_s0001.ridx │ ├── ts_0001_s0001.tdat │ ├── ts_0001_s0001.vidx │ └── ts_0001_s0001.vmet └── vid_0001.ticd ├── vid_0001.rdat ├── vid_0001.ridx └── vid_0001_s0001.tisd ├── vid_0001_s0001.rdat ├── vid_0001_s0001.ridx ├── vid_0001_s0001.vidx ├── vid_0001_s0001.vmet └── vid_0001_s0001_n0001.mp4 Cheers, Matt <MFO-Logo-GIF-small.gif> Matt Stead ***@***.*** > On Oct 18, 2024, at 7:08 AM, Remi Gau ***@***.***> wrote: > > > Can you point me to the MEF 3.0 example? > > AFAICT we do not have one > > — > Reply to this email directly, view it on GitHub <#469 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ATNKTHSTF7BWIY5YIZPH2L3Z4EB5VAVCNFSM6AAAAABQEIQVVOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRSGQ2DAMRYGQ>. > You are receiving this because you were mentioned. >

Remi-Gau · 2024-10-18T13:24:57Z

I think your dataset should be structured like this

├── dataset_description.json
├── README.md
└── sub-01
    └── sub-01_task-TaskName_ieeg.medd

where sub-01_task-TaskName_ieeg.medd is actually the test.medd from above.

Remi-Gau · 2024-10-18T13:27:19Z

but you are going to require some extra json files

see https://bids-specification.readthedocs.io/en/stable/modality-specific-files/intracranial-electroencephalography.html#sidecar-json-_ieegjson

effigies · 2024-10-18T13:37:10Z

@MEDFormat @Remi-Gau I've copied a pared down version of ieeg_epilepsy and replaced the _ieeg.* files with an _ieeg.medd directory and pushed to this PR.

Making some additional changes to adjust validator behavior, given that we aren't targeting the legacy validator and the schema changes havn't been merged yet.

Remi-Gau · 2024-11-04T17:43:45Z

ieeg_MED/README

maybe we should mention in the README that this dataset was mostly copied and adapted from another example: in case someone is looking for the 'real' BIDS dataset for this, otherwise they may think that we already have one that exist in the wild that they could have a look at.

Remi-Gau · 2024-11-04T17:45:47Z

ieeg_MED/dataset_description.json

+    "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": [


would also make sense to update the readme because of all the authors and institutions metadata: these people may otherwise wonder what dataset of theirs this one is linked to

feels easier than cleaning up all the dataset of any reference of the dataset it was copied from

effigies

@Remi-Gau WDYT?

.github/workflows/validate_datasets.yml

effigies · 2024-11-04T18:00:27Z

ieeg_MED/README

+Dataset description
+===================
+
+Example dataset demonstrating the [MED Format](https://medformat.org)


Suggested change

Dataset description

===================

Example dataset demonstrating the [MED Format](https://medformat.org)

MED Format demonstration

========================

Example dataset demonstrating the [MED Format](https://medformat.org).

This dataset is a copy of the [ieeg_epilepsy](../ieeg_epilepsy) example's raw data (run 1 only), replacing the BrainVision files with a `.medd/` directory.

effigies · 2024-11-05T13:06:28Z

ieeg_MED/dataset_description.json

+    "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/"
+    ]


Suggested change

"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/"

]

"Name": "MED Format example",

"BIDSVersion": "1.10.0",

"License": "CC0",

"Authors": [

"BIDS Contributors"

],

"ReferencesAndLinks": [

"../ieeg_epilepsy",

"https://medformat.org/"

]

.github/workflows/validate_datasets.yml

Add files via upload

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effigies added 4 commits October 18, 2024 09:29

Attempt to update test.medd to broadly follow ieeg_epilepsy

0771b30

Update scans.tsv

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Skip legacy validation

893fc5a

Import schema from branch that introduces MED format

969bb2d

effigies and others added 2 commits October 18, 2024 09:39

Typo in scans.tsv

abd0ea5

Merge branch 'master' into master

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effigies mentioned this pull request Nov 4, 2024

[ENH] Allow MED format for iEEG data (*_ieeg.medd/) bids-standard/bids-specification#1956

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MED example dataset (no data, only headers) #469

MED example dataset (no data, only headers) #469

MEDFormat commented Oct 17, 2024 •

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-Dataset description
-===================
-Example dataset demonstrating the [MED Format](https://medformat.org)
+MED Format demonstration
+========================
+Example dataset demonstrating the [MED Format](https://medformat.org).
+This dataset is a copy of the [ieeg_epilepsy](../ieeg_epilepsy) example's raw data (run 1 only), replacing the BrainVision files with a `.medd/` directory.

MED example dataset (no data, only headers) #469

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MED example dataset (no data, only headers) #469

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effigies Nov 4, 2024

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effigies Nov 5, 2024

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MEDFormat commented Oct 17, 2024 •

edited by Remi-Gau

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