Kernel Portal Pipelines Release Notes

All notable changes to pipelines served in the Kernel Portal will be documented here. See Data Export Pipelines and Data Analysis Pipelines for descriptions of each pipeline.

SNIRF and NIfTI exports are tagged with the version of the Portal pipeline that produced them, as YYYY.MM.DD. This tag can be found under nirs/metaDataTags/KernelPortalVersion in the SNIRF files; and in the “descrip” field of the NIfTI header.

2024-11-19

Fixed

• Reconstruction: the "sum" moment was erroneously excluded from participating to reconstruction outputs since the `2024-08-27` release
• QC NIRS Basic: high baseline threshold updated to count offending detectors, rather than modules

2024-10-23

Changed

• SNIRF: Hb Moments, Analysis NIRS GLM, and Analysis NIRS Epoched: restore short channel regression to previous defaults (take mean of signal, use corresponding layer) until further investigation
• QC NIRS Basic: only warn about missing response events for Kernel tasks that are expected to have response events
• Upgrade Python (3.8.12 -> 3.11.7), and upgrade all dependencies to versions that support Python 3.11

2024-09-20

Added

• SNIRF (all): landmarks LPA, RPA, Nz are added for all Flow2 SNIRF exports. These are expected by e.g. Cedalion for plotting topoplots.
• SNIRF: Hb Moments: add optional dataUnit (µM)
• SNIRF: Moments: add optional dataUnit (ps for mean, ps² for variance)

Changed

• SNIRF (all): bad channels are no longer filled with NaNs. As a result, the SNIRF files are much smaller.
• SNIRF: Hb Moments, Analysis NIRS GLM, and Analysis NIRS Epoched: short channel regression is using the first PC instead of the mean across short channels

Fixed

• SNIRF: Hb Moments: `offset` field renamed `dataOffset` per the specification

2024-08-28

Changed

• Analysis Task: always export task events and task raw events, whether a task analysis is implemented or not
• Analysis: Task: rename exports task_events.tsv and task_metrics.json with the canonical prefix

Fixed

• SNIRF: Gated: make `timeDelayWidths` an array of widths (rather than a single float)

2024-07-23

Added

• Analysis NIRS GLM: added support for retinotopy task
• QC: Syncbox: added daq QC section

Fixed

• QC: Syncbox: fixed reading of SyncBox tensor

2024-07-06

Fixed

• SNIRF: Hb Moments: fixed rare floating-point bug in absolute pipeline

2024-06-27

Changed

• SNIRF: absolute HbO/HbR are only computed in SNIRF: Hb Moments pipeline
• SNIRF: Hb Moments: absolute HbO/HbR are reported in the dataOffset field instead of as an auxiliary stream
• SNIRF: Hb Moments: absolute HbO/HbR use 100 samples throughout the session that are not contaminated by motion, instead of the first 30s of the session.

Removed

• All pipelines: Flow1/Gamma support discontinued

2024-05-17

Added

• QC: NIRS Expert: new topoplot showing channels with a heart rate that deviates from the median heart rate, indicating channels that may not be making good contact

Changed

• SNIRF: in the absence of an alignment stream, use default shifts to enable curve fitting and absolute Hb estimates
• QC: NIRS Expert: motion scoring percentiles updated using TRUST study data

2024-05-14

Added

• Reconstruction: new pipeline for Flow2, using moments

Removed

•  Reconstruction: remove MindsEye visualization and GLM MindsEye snapshots

2024-03-05

Changed

• SNIRF: Add plate names

Fixed

• QC: NIRS: correct reporting of dropped packets
• QC: NIRS Expert: remove channels with bad Scalp Coupling Index (SCI) to compute physiology
• QC: NIRS Expert: better error handling for plots
• SNIRF: NIRS: data now starts at time=0 (for MNE compatibility)

2024-02-01

Added

•  SNIRF: more session metadata