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Data Structure

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Taiyou edited this page Jan 24, 2026 · 1 revision

Data Structure

Directory Overview

OptofMRI_5HT/
├── data/                    # Main data directory
│   ├── session1/           # Session 1 preprocessed time series
│   ├── session2/           # Session 2 preprocessed time series
│   ├── session3/           # Session 3 preprocessed time series
│   ├── session4/           # Session 4 preprocessed time series
│   ├── COPEResults/        # GLM analysis results (COPE values)
│   └── notUsed/            # Archived/unused data files
├── ROIs/                    # 28 Region of Interest masks
├── 5HTR/                    # 5-HT receptor expression maps
├── AllenBrainAtlas/        # Allen Brain Atlas reference files
├── figures/                 # Generated figures
├── programs/               # Analysis functions
├── preprocessing_templates/ # SPM preprocessing templates
├── motion_artefacts/       # Motion artifact reports
└── behavioralExp/          # Behavioral experiment data

Session Data

Time Series Data (data/sessionX/)

Each session folder contains preprocessed fMRI time series for each subject:

File Pattern Description
TPH*_main_preprocessed.mat Transgenic (TPH-Cre) mouse data
WT*_main_preprocessed.mat Wild-type control mouse data

Data structure within .mat files:

  • timeseries_blue: Time series during blue light stimulation
  • timeseries_yellow: Time series during yellow light control
  • Format: [time × ROI] matrix

COPE Results (data/COPEResults/)

Contrast of Parameter Estimates from GLM analysis:

File Description
COPE_session1_tph_blue.mat TPH group, blue stimulation, Session 1
COPE_session1_tph_yellow.mat TPH group, yellow control, Session 1
COPE_session1_cont_blue.mat Control group, blue stimulation, Session 1
COPE_session1_cont_yellow.mat Control group, yellow control, Session 1
tphB_session*.mat TPH blue COPE values for each session
tphY_session*.mat TPH yellow COPE values for each session
CONTB_session*.mat Control blue COPE values for each session
CONTY_session*.mat Control yellow COPE values for each session
pval_*.mat Statistical comparison p-values

COPE data structure:

  • Matrix format: [nSubjects × nROIs]
  • 28 ROIs per subject
  • Values represent mean beta estimates within each ROI

Individual NIfTI Files (data/COPEResults/sessionX/BLUE/ and /YELLOW/)

Individual subject contrast maps in NIfTI format:

  • TPH*_positiveBlue_20.nii: Positive contrast for blue stimulation
  • WT*_positiveBlue_20.nii: Control subject positive contrast

ROI Masks (ROIs/)

28 bilateral brain region masks in NIfTI format:

ID Region Abbreviation
01 Frontal Pole FP
02 Orbitofrontal Cortex OFC
03 Medial Prefrontal Cortex mPFC
04 Secondary Motor Cortex M2
05 Anterior Cingulate Cortex ACC
06 Primary Motor Cortex M1
07 Somatosensory Cortex SS
08 Ventral Retrosplenial Cortex vRSC
09 Dorsal Retrosplenial Cortex dRSC
10 Temporal Association Area TAA
11 Primary Auditory Cortex A1
12 Primary Somatosensory Cortex S1
13 Posterior Parietal Association PPA
14 Primary Visual Cortex V1
15 Nucleus Accumbens NAc
16 Caudate Putamen CPu
17 Bed Nucleus of Stria Terminalis BST
18 Globus Pallidus External GPe
19 Globus Pallidus Internal GPi
20 Reticular Thalamus RT
21 Ventral Pallidum VP
22 Dentate Gyrus DG
23 CA1 CA1
24 Lateral Habenula LHb
25 Substantia Nigra pars reticulata SNr
26 Ventral Tegmental Area VTA
27 Median Raphe Nucleus MRN
28 Dorsal Raphe Nucleus DRN

5-HT Receptor Maps (5HTR/)

Allen Brain Atlas-derived receptor expression maps:

File Receptor
htr1a.nii 5-HT1A receptor
htr1b.nii 5-HT1B receptor
htr1f.nii 5-HT1F receptor
htr2a.nii 5-HT2A receptor
htr2c.nii 5-HT2C receptor
htrproj.nii Serotonergic projection density

Allen Brain Atlas Files (AllenBrainAtlas/)

File Description
resampledAtlas.nii Resampled anatomical template
resampledAnno.nii Resampled annotation/parcellation
AllenAtlasNorm.r R script for atlas normalization

Motion Artifact Reports (motion_artefacts/)

Text files containing framewise displacement values:

  • session1/TPH*_fd.txt, session1/WT*_fd.txt
  • Similar structure for sessions 2-4
  • Used for quality control and subject exclusion

Output Figures (figures/)

Generated publication figures organized by figure number:

  • Figure2/: Main COPE results
  • FigureS4/, FigureS5/, etc.: Supplementary figures

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