From 93d9acef2ad8b2a0e7619bad23f2c34cef52a0e9 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Thu, 26 Oct 2023 09:52:10 -0500 Subject: [PATCH] Updated Whats New with score preprint --- docs/source/DocumentationSummary.md | 13 ++++++++++-- docs/source/WhatsNew.md | 5 +++++ .../bids/validate_bids_dataset.ipynb | 20 ++++++++++++------- .../matlab_scripts/web_services/runAllTests.m | 2 +- 4 files changed, 30 insertions(+), 10 deletions(-) diff --git a/docs/source/DocumentationSummary.md b/docs/source/DocumentationSummary.md index 7849048..17c8a76 100644 --- a/docs/source/DocumentationSummary.md +++ b/docs/source/DocumentationSummary.md @@ -19,14 +19,23 @@ Detailed case study in using HED-3G for tagging: > NeuroImage Special Issue Practice in MEEG. NeuroImage 245 (2021) 118766. > [https://www.sciencedirect.com/science/article/pii/S1053811921010387](https://www.sciencedirect.com/science/article/pii/S1053811921010387). +### Preprints + +Hierarchical Event Descriptor library schema for EEG data annotation: + +> Pal Attia, T., Robbins, K., Beniczky, S., Bosch-Bayard, J., Delorme, A., Lundstrom, B., Rogers, C., Rampp, S., +> Valdes-Sosa, P., Truong, D., Worrell, G., Makeig, S., and D. Hermes (2023). +> [**https://arxiv.org/abs/2310.15173**](https://arxiv.org/abs/2310.15173). +> DOI:10.48550/arXiv.2310.15173. + Framework for annotating and analyzing events in context: > Makeig, S. and K. Robbins (2023 under review). > Events in context - A framework for the study of brain, experience and behavior. > **Preprint**: [**https://psyarxiv.com/e7jbm**](https://psyarxiv.com/e7jbm) -> DOI: 10.31234/osf.io/e7jbm +> DOI: 10.31234/osf.io/e7jbm. -### Book chapters +### Book chapters (preprints) > Truong, D., Robbins, K., Delorme, A., and S. Makeig (in press). > End-to-end processing of M/EEG data with BIDS, HED, and EEGLAB. diff --git a/docs/source/WhatsNew.md b/docs/source/WhatsNew.md index 66a2fd0..84bc913 100644 --- a/docs/source/WhatsNew.md +++ b/docs/source/WhatsNew.md @@ -4,6 +4,11 @@ Upcoming... **Nov. 10-17, 2023 sFN (Society for Neuroscience)** in Washington D.C.: > **Visit SCCN booth (#3031)** for help and information (or just to visit) about **NEMAR/OpenNeuro**, **EEGLAB**, **HED**, **LSL**, and **MoBI**. +**October 4, 2023**: **New HED preprint Score HED library** +> Hierarchical Event Descriptor library schema for EEG data annotation +> by Pal Attia, T., Robbins, K., Beniczky, S., Bosch-Bayard, J., Delorme, A., Lundstrom, B., Rogers, C., Rampp, S., Valdes-Sosa, P., Truong, D., Worrell, G., Makeig, S., and D. Hermes (2023). +> **Preprint**: [**https://arxiv.org/abs/2310.15173**](https://arxiv.org/abs/2310.15173). +> DOI:10.48550/arXiv.2310.15173. **September 20, 2023 16:00 CEST**: **INCF Workshop on HED and BIDS** > Event annotation in neuroimaging using HED: from experiment to analysis diff --git a/hedcode/jupyter_notebooks/bids/validate_bids_dataset.ipynb b/hedcode/jupyter_notebooks/bids/validate_bids_dataset.ipynb index b05e536..7a99c75 100644 --- a/hedcode/jupyter_notebooks/bids/validate_bids_dataset.ipynb +++ b/hedcode/jupyter_notebooks/bids/validate_bids_dataset.ipynb @@ -32,15 +32,21 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 3, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Using HEDTOOLS version: {'date': '2023-10-12T10:29:43-0500', 'dirty': True, 'error': None, 'full-revisionid': 'e9e63e39f6a99487c5e69ae96e653c4580045ec0', 'version': '0.3.0+164.ge9e63e3.dirty'}\n", - "HED Examples version: {'version': '0.2.0+173.g63d5080.dirty', 'full-revisionid': '63d50808c4c7e97bdfc89076cb19af9e13252057', 'dirty': True, 'error': None, 'date': '2023-10-23T11:09:31-0500'}\n", - "No HED validation errors\n" + "HED Examples version: {'version': '0.2.0+177.g642dd60.dirty', 'full-revisionid': '642dd607a2fa508f64985afaa8a040b31023ee92', 'dirty': True, 'error': None, 'date': '2023-10-24T15:09:52-0500'}\n", + "HED validation errors: \n", + "\n", + "Errors in file 'sub-02_ses-01_task-DriveRandomSound_run-1_events.tsv'\n", + "\tIssues in row 2833:\n", + "\t\thed string: (Def/Non-cue-sound, Onset),(Def/Drive-vehicle, Offset),(Def/Trial-marker, Offset),(Def/Non-cue-sound, Offset),(Def/Show-speed-sign/45, Offset)\n", + "\t\t\tONSET_OFFSET_INSET_ERROR: 'Offset' uses name 'Non-cue-sound', which was already used at this onset time. Problem spans string indexes: 102, 108\n", + "\t\t\tONSET_OFFSET_INSET_ERROR: Offset tag 'Def/Show-speed-sign/45' does not have a matching onset. Problem spans string indexes: 111, 133\n" ] } ], @@ -55,8 +61,8 @@ "\n", "## Set the dataset location and the check_for_warnings flag\n", "check_for_warnings = False\n", - "dataset_path = 't:/summaryTests/ds002718-download'\n", - "outfile = 't:/ds002718_errors.txt'\n", + "dataset_path = 't:/summaryTests/ds004105-download'\n", + "outfile = 't:/ds004105_errors.txt'\n", "## Validate the dataset\n", "bids = BidsDataset(dataset_path)\n", "issue_list = bids.validate(check_for_warnings=check_for_warnings)\n", @@ -72,8 +78,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2023-10-24T18:51:33.095713100Z", - "start_time": "2023-10-24T18:51:31.396158Z" + "end_time": "2023-10-24T22:15:17.741340200Z", + "start_time": "2023-10-24T22:14:12.987247500Z" } } } diff --git a/hedcode/matlab_scripts/web_services/runAllTests.m b/hedcode/matlab_scripts/web_services/runAllTests.m index 6e1062d..52cd415 100644 --- a/hedcode/matlab_scripts/web_services/runAllTests.m +++ b/hedcode/matlab_scripts/web_services/runAllTests.m @@ -1,6 +1,6 @@ host = 'https://hedtools.org/hed'; host = 'https://hedtools.org/hed_dev'; -%host = 'http://127.0.0.1:5000'; +host = 'http://127.0.0.1:5000'; errorMap = containers.Map('KeyType', 'char', 'ValueType', 'any');