NeuroDOT v1.4

Changes since NeuroDOT v1.3:

1. GUIs

• NeuroDOT Render Tool: interactive GUI to select a NIfTI or 4dfp overlay and render the data on a default or custom cortical mesh. Alternatively, data may be passed to the app directly from the command line or from within a script.

2. Format Compatibility updates:

• SaveVolumetricData: added option for saving in nii.gz format
• snirf2ndot: updated to work on variables in the workspace, in addition to optionally accepting file inputs
• lumo2ndot: added compatibility with Gowerlabs LUMO systems

3. New Support Files:

• Added Glasser and Schaefer Parcellation files to Support Files: Glasser_2016_Parcels.nii, Glasser_12nets_360parcels_on_MNI.mat, Schaefer2018_7nets_300parcels_on_MNI.mat, Schaefer2018_7nets_400parcels_on_MNI.mat, and Schaefer2018_17nets_400parcels_on_MNI.mat

4. Other function updates:

• Resample_Vol_to_Parcel: resamples data to a single time trace for each parcel in the field of view of a specified volume
• Plot_RawData_Cap_DQC: added new layouts for "tall" arrays in 2D; fixed colorbar orientation for arrays with single source-detector separation distances.
• Plot_RawData_Metrics_II_DQC: added params.logfft to plot power spectrum on log-log axes; by default, both axes will be logarithmic; to set the y-axis to be linear, set params.logfft = 0

5. Tutorial & Documentation updates:

• Tutorial for Participant Specific Head Modeling
  • Utilizes FreeSurfer 7.2 recon_all segmentation routine, compatible with Linux OS (CentOS6, CentOS7, CentOS8, and Ubuntu18)
    • Mac OS compatibility coming soon!
  • Excluding FreeSurfer, the script is compatible with Windows and Mac operating systems.
• Updated contact information and created feedback and user registration forms
• Contact NeuroDOT development team: [email protected]
• NeuroDOT feedback: https://forms.gle/iEYfEZhfj99FVEs29
• NeuroDOT user registration: https://tinyurl.com/NeuroDOT

NeuroDOT v1.3

Changes since NeuroDOT v1.2:

1. Updates to Visualization functions:

• PlotCapData: updated source/detector spacing
• PlotMeshSurface: fixed facecolor parameter for case without data
• PlotSlices, PlotSlice, PlotSlicesTimeTrace: adjusted colorbar settings, added white background ‘bgW’ parameter
• Plot_RawData_Metrics_I_DQC: added params.LFO_GI to select which measurments to show in LFO plot
• Applycmap: compatibility with params.BG when all elements are equal to zero
• Adjust_brain_pos, PlotLRMeshes, PlotMeshSurface: added flat map ‘Fnodes’ case
• Plot_RawData_Cap_DQC, PlotCapPhysiologyPower: fixed SNR DQ metrics to compute based on the correct method
• DrawColoredSynchPoints: added colors to plot for up to 7 different pulses

2. Format Compatibility updates:

• Snirf2ndot & Nirs2ndot: enforce column organization of optode position arrays
• LoadVolumetricData, SaveVolumetricData, Nifti_4dfp: compatibility with volumetric data in sagittal and coronal orientations, compatibility with 4D data
• Updated all functions using info.pairs and info.MEAS to be compatible with tables

3. Other function updates:

• GLM_181206: Added R squared output
• Added ParcelBased_fc function
• Added Matrix_Org3 and freezeColors functions to Visualizations

4. Tutorial & Documentation updates:

• Light Modeling: updated all light modeling scripts to use makeAnirfaster, added tutorial for Light Modeling with a subset of measurements, and added tutorial for Light Modeling with a split-pad layout
• Loading Raw Data script and PowerPoint added for loading .snirf, .nirs, and .mat data
• Added Script_for_Viewing_Parcels for parcel-based functional-connectivity analysis
• Added NeuroDOT Tutorials ReadMe file
• Updated NeuroDOT Quick Start Guide

NeuroDOT v1.2

Changes since NeuroDOT v1.1:

1. Compatibility with SNIRF format:

• Updated info.paradigm.synchpt creation in snirf2ndot
• Added ndot2snirf to convert from NeuroDOT format to SNIRF format
• Verified compatibility with LUMO

2. Added NIRS format compatibility:

• nirs2ndot to convert data from .nirs files to be used in NeuroDOT
• ndot2nirs to convert NeuroDOT data to .nirs format

3. Added NIFTI format compatibility:

• Added nifti_4dfp to convert between .nii and .4dfp format
• Updated LoadVolumetricData and SaveVolumetricData to be compatible with .nii files
• Fixed compatibility with ‘nii.gz’ extension

4. Added new functions:

• Visualizations: AdjustFoci, Draw_ROIs_on_Cortex, Nuisance_Regress, PlotCapMeasSpaceData_Pairs, Two_D_Image_hist,
  GrayPlot_TimeTrace_Rsd_by_WL
• Light Modeling: OptProp, PSF_Metrics_200630, threshold5R_new, calc_NN, Generate_pad_from_grid
• Spatial Transforms: resample_A_to_atlas
• Reconstruction: MBLL

5. Updated NeuroDOT Tutorial PowerPoints and Scripts:

• AlignMe tutorials
• Script for Generating a Pad File
• Full Data Processing Overview
• Visualization Overview

6. Updates to AlignMe:

• Updated method for scaling from atlas to participant measurements
• Updated transform to match pre-multiply convention

NeuroDOT v1.1

Added converter from SNIRF to NeuroDOT data format and loading/saving compatibility with NIFTI. Additionally, updates have been made to the NeuroDOT tutorials, and a new GUI for Head Modeling, AlignMe, has been added.

NeuroDOT Release v1.0

Official release of NeuroDOT, an extensible Matlab toolbox for efficient optical brain mapping.

More details, support files, and documentation are available at:
https://www.nitrc.org/projects/neurodot