TimeSeries BIDS converted

TimeSeries_BIDS
================

Dataset overview
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This repository contains an fNIRS dataset organized in Brain Imaging Data Structure (BIDS) format, with 18 participants and two sessions per participant.

- Dataset name: TimeSeries BIDS converted
- BIDS version declared in dataset description: 1.7.0
- Participants listed in participants.tsv: 18 (sub-01 to sub-18)
- Sessions: ses-01 and ses-02 for each participant

Primary BIDS files
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- dataset_description.json
- participants.tsv
- sub-*/ses-*/nirs/*

Derivative data
---------------
Processed outputs are stored under derivatives/converted_nirs/ and follow subject/session nesting:

- derivatives/converted_nirs/sub-XX/ses-YY/

Code and analysis scripts
-------------------------
MATLAB scripts used for reliability/statistical analysis and figure generation are in code/.
The scripts are figure-oriented and named to match manuscript figures.

Main analysis groups:

1) RSFC matrix reliability and visualization
- Fig2_toPlotMeanCorrMatrix_linecorre_18subs.m
- Fig3_calTRTofRSFC_18subs.m
- Fig3_toPlot_ICCofRSFC_ANDbar_HbORT.m
- FigS1_toPlotlineCorr_betweenICC_RSFC.m

2) Global network metric ICC and statistics
- Fig4_cal_globICC_usingAll_S.m
- Fig4_Toplot_globICC_S_10metrics.m
- Fig5_cal_globICC_usingAUC.m
- Fig5_toPlot1_globICCbar_HbORT_MeanStd_useAUC.m
- Fig5_toPlot3sub_globICCbar_HbORT_MeanStd_useAUC.m
- Fig5_anova_ICC10globMetrics_ifHbORT.m
- Fig5_NEWpairTtest_ICC10globMetrics_ifHbORT.m

3) Nodal metric ICC and statistics
- Fig6_calANDplot_nodalICC_usingAll_S.m
- Fig8_cal_nodalICC_usingAUC.m
- Fig8A_toPlot_nodeICCbar_HbORT_MeanStd_useAUC.m
- Fig8B_toPlot_nodeICCbar_HbORT_MeanStd_useAUC.m
- Fig8A_NEWpairTtest_whichMetricBetter_inEachHbORT.m
- Fig8B_NEWpairTtest_whichHbBetter_inEachNetMetric.m
- Fig8_anova2_nodalTRT_Measures_HbORT.m

Analysis dependencies
---------------------
The MATLAB scripts depend on additional .mat files and helper functions that are not guaranteed to be present in raw BIDS folders.
Examples referenced by scripts include:

- TRTcorrMatrix_18subs2Times.mat
- ICC_ofRSFC_HbORT_18subs.mat
- TRT_HbO_NetworkMetrics_revisBeta.mat
- TRT_HbR_NetworkMetrics_revisBeta.mat
- TRT_HbT_NetworkMetrics_revisBeta.mat
- HbO_NetworkProperties.mat
- HbR_NetworkProperties.mat
- HbT_NetworkProperties.mat
- ICCforbar_10globlMetrics_fromAUC_HbORT.mat
- ICCforbar_46nodeForMeanStd_fromAUC_HbORT.mat

Additional MATLAB functions called by scripts:

- IPN_icc
- anova_rm
- rm_anova2

Before running code/, make sure these files/functions are available on the MATLAB path.

BIDS compliance notes
---------------------
This dataset is structured as a BIDS dataset at the top level (dataset_description.json, participants.tsv, sub-*/ses-*/nirs, derivatives/).

For public release and strict validation, confirm the following:

1) All required *_nirs.json sidecars are complete and consistent.
2) Channel metadata and source-detector mapping are valid.
3) Event and participant metadata fields are complete where applicable.
4) Dataset passes bids-validator without errors (warnings reviewed case by case).

Suggested validation command
----------------------------
Run BIDS Validator from the dataset root:

bids-validator .

Known scope of this repository
------------------------------
- Raw and derivative BIDS-like directory structure is present.
- Figure/statistical scripts in code/ are analysis-specific and use external intermediate MATLAB files.
- Reproducing all figures requires the referenced intermediate .mat files and helper functions.

Contact and citation
--------------------
Authors listed in dataset_description.json:

- Niu, Haijing
- Zheng, Sha
- Yuan, Haodong

If this dataset is used in publications, cite the corresponding study and include dataset version/date used.