NeuroDOT News

NeuroDOT (v1.4) and NeuroDOT_py (v1.0.0) Releases

Emma Speh — Wed, 23 Oct 2024 9:09:53 GMT

We are excited to announce the latest NeuroDOT (v1.4) & NeuroDOT_py (v1.0.0) releases on GitHub and PyPi! The Matlab release features improvements to format compatibility with NIfTI, SNIRF, and LUMO, a new tutorial for participant-specific head modeling, and an interactive user-interface for rendering data on a mesh. For NeuroDOT_py, a Sphinx-based documentation site is now available in addition to the toolbox being available via PyPi. This release was made possible thanks to the efforts of the NeuroDOT Development Team and the Brain Light Lab at WashU.

Become a registered NeuroDOT user to receive development updates, news about workshops, and individual help from the NeuroDOT team: https://tinyurl.com/NeuroDOT

The advancements represented in this update were supported by the National Institute of Neurological Disorders and Stroke (NINDS) of The National Institutes of Health under Award Number U24NS136402. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

NeuroDOT Request for Feedback

Emma Speh — Tue, 12 Mar 2024 3:44:33 GMT

NeuroDOT is actively interested in obtaining community feedback engagement on our GitHub page (https://github.com/WUSTL-ORL/NeuroDOT), the openfNIRS forum (https://openfnirs.org/community/neurodot-forum/), and here on NITRC.

If you have any suggestions or questions regarding NeuroDOT, please submit your feedback through this Google Form: https://forms.gle/iEYfEZhfj99FVEs29

-Emma Speh

New GitHub Release: NeuroDOT v1.3

Emma Speh — Wed, 06 Mar 2024 2:36:49 GMT

Latest NeuroDOT release, v1.3, is now available from GitHub.

Changes since version 1.3 include:

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

New GitHub Release: NeuroDOT v1.2

Emma Speh — Wed, 05 Jul 2023 1:07:12 GMT

Latest NeuroDOT release, v1.2, is now available from GitHub.

Changes since version 1.1 include:
Updated compatibility with SNIRF format
Added NIRS format compatibility
Added NIFTI format compatibility
Updated NeuroDOT Tutorial PowerPoints and Scripts
Updates to AlignMe

NeuroDOT Tutorials Available to Download

Emma Speh — Tue, 27 Jun 2023 2:23:28 GMT

Updated versions of each NeuroDOT tutorial PowerPoint and accompanying Matlab script can be downloaded here, or from GitHub (https://github.com/WUSTL-ORL/NeuroDOT).

Schroeder et al. 2023 Language Production data to be posted

Emma Speh — Wed, 14 Jun 2023 12:52:45 GMT

The paper, https://doi.org/10.1016/j.neuroimage.2023.120190 was recently published.

The data used for this paper will be posted here in the SNIRF format in the next few weeks.

Resting State Dataset released

Emma Speh — Wed, 08 Mar 2023 1:43:42 GMT

9 resting state datasets collected using a HD-DOT system at Washington University in St. Louis, packaged using NeuroDOT. To download, you will need to be signed in to a NITRC account.

AT Eggebrecht et al., "Mapping distributed brain function and networks with diffuse optical tomography," Nature Photonics, 8, 448-454 (2014).

sfNIRS Workshop Preparation Materials

Emma Speh — Thu, 06 Oct 2022 5:58:25 GMT

A file has been uploaded to the package 'sfNIRS 2022 Workshop' detailing steps for those who will be attending the educational course: 'Diffuse Optical Mapping of Human Brain Function using NIRFAST and NeuroDOT: A Hands-on course' at the sfNIRS conference in Boston, MA on 10/8 from 2:00pm-4:50pm EST.

NeuroDOT_py for Pre Processing Release

Emma Speh — Wed, 15 Jun 2022 7:09:47 GMT

The GitHub repository for NeuroDOT_py is available, as it is currently in development, to be used for the 'Data Pre Processing and Temporal Analyses' section of the educational course at OHBM 2022.