NITRC Community News

NBS-Predict v1.0.0-beta.12 released

Emin Serin — Thu, 04 Apr 2024 1:27:22 GMT

We reintroduced leave-one-out cross-validation (LOOCV) to classification and fixed minor bugs in our GUI. Note that LOOCV is not available for regression.

Don't hesitate to try out our updated features and take your data analysis to the next level!

SOBP BrainHack, May 7-8, 2024, Austin TX

David Kennedy — Tue, 26 Mar 2024 12:01:29 GMT

Going to Society of Biological Psychiatry (SOBP) annual meeting this May? Want more time to think? Want more time to code? Want more time to collaborate? The SOBP BrainHack is the place to be! May 7th&8th, 2024.

Details at https://www.repronim.org/SOBPHack-052024/;
Registration at https://www.eventbrite.com/e/sobp-brain-hack-tickets-857174581247?aff=oddtdtcreator.

Space is limited, register soon!

NITRC 2.1.68 released

NITRC Moderator — Thu, 21 Mar 2024 4:13:05 GMT

We are pleased to announce the release of NITRC Version 2.1.68.

This release features the import of GitHub topics to NITRC tool categorizations. NITRC administrators are encouraged to link to GitHub projects, if applicable, to automatically update NITRC with GitHub project information and releases.

This release also includes a number of usability bug fixes.

Release notes can be found at https://www.nitrc.org/plugins/mwiki/index.php?title=nitrc:NITRC_Release_Notes#NITRC-R_Release_v2.1.68-0_-_03.2F06.2F2024

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

March Data Sharing and Reuse Seminar

David Kennedy — Fri, 08 Mar 2024 3:02:37 GMT

Join NIH Office of Data Science Strategy (ODSS) at the March Data Sharing and Reuse Seminar!
Dr. Kilian Pohl will present "Accelerating Neuroscience Discovery Using Shared Software and Data" on March 8, 2024, at 12 p.m.

The monthly series highlights researchers who have taken existing data and found clever ways to reuse the data or generate new findings. A different NIH institute or center will also share its data science activities each month.

Event Date: Friday March 8, 2024, from 12-1 p.m.

Register at:
https://datascience.nih.gov/content/march-data-sharing-and-reuse-seminar

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

MIITRA labels are here!

Konstantinos Arfanakis — Wed, 21 Feb 2024 4:55:07 GMT

Version 3 of the MIITRA atlas is now available and contains labels!

Labels from a total of 30 labeling schemes / atlases are now available in MIITRA space (both in 1mm and 0.5mm resolution) e.g. AAL, Brodmann, Desikan-Killiany, von Economo, HCP, Julich, Shen, Yeo labels just to name a few. To generate them, labels from 30 different labeling schemes / atlases were applied to all 400 older adult participants of the MIITRA atlas in native space, then all labels were transformed to MIITRA space, and majority voting was used to generate the final labels in MIITRA space. The sets of labels made available in this version are based on structural, cytoarchitectonic, and functional connectivity information and substantially enhance the functionality of the MIITRA atlas.

In addition, the new version of the atlas includes gray matter masks and a new manual.

Online CONN 2024 workshop registration open

Alfonso Nieto-Castanon — Tue, 13 Feb 2024 3:31:14 GMT

We are pleased to announce that registration for the CONN 2024 functional connectivity workshop is now open. This workshop will take place ONLINE over ten consecutive Fridays with weekly 3-½ hour classes from 11am to 2:30pm EDT (UTC−04:00), starting on Friday April 5 and ending on Friday June 7 2024 (see https://courses.conn-toolbox.org/course-schedule for the course schedule details).

The CONN toolbox workshop offers intensive hands-on and highly interactive courses covering all aspects of functional connectivity analyses in CONN, and both beginners and advanced users are welcome. Classes take place over Zoom on Fridays for ten consecutive weeks. Zoom meetings of each class are recorded and made available to students to view at any time during the course. There are also practice homework assignments, and faculty is available during office-hour segments for additional student questions or support.

For additional information and registration see https://courses.conn-toolbox.org

Thank you for your support!
Alfonso Nieto-Castanon

ICH_PHE_Segmentation Lite v1.0 released

anhtrn — Tue, 06 Feb 2024 3:08:45 GMT

GUI and small model CNN for segmentation

Reminder: ReproNim/INCF Fellowship program

David Kennedy — Mon, 29 Jan 2024 5:24:29 GMT

Time is running out. Apply now! Deadline is Jan 31.

The ReproNim/INCF Fellowship program is ready to select the fourth cadre of Fellows! Applications are now open here: https://docs.google.com/forms/d/e/1FAIpQ... We will award five to ten fellowships for this year; the total number of Fellows pending availability of funds. Mark your calendar for application submission starting January 1 through January 31, 2024. We will conduct a hybrid kickoff workshop held in conjunction with the OHBM BrainHack, typically preceding the OHBM annual conference which is scheduled for June 23-27, 2024 in Seoul, South Korea. Some travel assistance may be available to the Fellows.

For more information about the Fellowship program, here: https://www.repronim.org/fellowship. Note: Prior applicants who were not selected last year are welcome to re-apply!