Change History

All notable changes to these SOPs are documented below, starting with the most recent version of the document.

You found an error

If you want to check the list of open issues, please proceed to our issue tracker.

If you have identified a problem, a typo, or something missing, and you know it is not in our tracker, please report it by creating a new issue.

0.5.0 (June 12, 2026)

Compare with 0.4.2

This release consolidates roughly two years of work — the bulk of the HCPh data collection, the full functional- and structural-connectivity analysis, and a security-hardened, reproducible documentation build. Changes are grouped by theme; only milestone pull requests (and a few individual commits) are linked.

Connectivity analysis & reliability

• Functional-connectivity (FC) estimation and variability analyses, covering sparse inverse-covariance estimation and intra-/inter-scanner reliability quantified with the intraclass correlation coefficient (ICC) (#549, #551, #553).
• Bayesian modeling of structural-connectivity (SC) reliability, with a standalone worked example (#528, #537).
• FC-matrix loading and confound retrieval refactored into reusable load_save/confounds modules, and mood/state-questionnaire parsing to derive analysis confounds (sleep, caffeine, room environment) from the study's issue templates (#523, #527, #557).

Generalizability (multi-scanner) protocol

• SOPs for the multi-scanner "generalizability" acquisitions (Prisma / Vida / VidaFit), including scanner-specific handling of the alarm screen, audio system, and console unlocking, plus standardized protocols and scan durations (#493, #495, #497).
• Wave-2 recruitment and scheduling adjustments (#499).

Eye-tracking

• End-to-end eye-tracking → BIDS conversion and screening/QC guidance, including a revised conversion pipeline and drift handling (#459).

Physiological recordings

• BIOPAC/AcqKnowledge handling and physiological → BIDS conversion, including splitting multi-run AcqKnowledge files (#506); clarified ECG calibration instructions (#539).

Data management with DataLad

• DataLad-based data management on the Curnagl HPC cluster, derivatives organized as subdatasets, and a BIDS indexer driving data intake (#507, #522, #542).

Preprocessing on HPC

• fMRIPrep on Curnagl (SLURM): anatomical-only runs, micromamba environments, and TemplateFlow pre-download for offline compute nodes (#508, #516, #519).

Quality control

• QC/QA criteria for unprocessed and preprocessed data and for functional connectivity, and an analysis of the manual image-rating experience (#469).

Manuscript, figures & references

• Registered-report figures and machinery to save figure captions for automatic generation of the paper's supplementary material (#544); clarified methods (e.g. atlas dimensionality vs. number of regions) and a README listing the datasets required to reproduce the analyses (#555, #559); a documented data-release checklist (#538).

Site infrastructure, CI & build

• Security: removed the compromised polyfill.io CDN — sold in 2024 and serving malware — from the MathJax configuration (#562).
• Modernized and pinned the MkDocs/Material stack for reproducible builds, dropped the unmaintained mkpdfs PDF fork, and pinned the MathJax CDN with Subresource Integrity (#562); repaired the deploy/codespell CI workflows and fixed broken links and spelling (#550, #564).

0.4.2 (September 27, 2023)

Compare with 0.4.1

Bug fixes

• CITATION.cff (f36b24a by Oscar Esteban).
• Trying to hold my temper with Zenodo (c118518 by Oscar Esteban).

0.4.1 (September 27, 2023)

Compare with 0.4.0

0.4.0 (September 27, 2023)

Compare with 0.3.0

Enhancements, new features, and additions

• Add report pre-registered on OSF and fix references (f9a8360 by Oscar Esteban).
• Replace --merge true with --how merge in datalad updates (d297d45 by Oscar Esteban).
• Add DataLad documentation for synchronizing and adding new data (5d57e74 by Oscar Esteban).
• Add a .zenodo.json with the intent of connecting Zenodo (ee429ea by Oscar Esteban).
• Play nice with Apache license in heuristic, better documentation (2dffffc by Oscar Esteban).

Bug Fixes

• Datalad DOI and link (fc63118 by Oscar Esteban).
• Escape HTML special characters (e54c468 by Oscar Esteban).
• Escaping characters (737edce by Oscar Esteban).
• Remaining bugs in heuristic file (443493c by Oscar Esteban). Related issues/PRs: #179
• Revise heuristic after testing it (ca49867 by Oscar Esteban).
• Overhaul of the data-management section with DataLad (5afcd97 by Oscar Esteban). Related issues/PRs: #100, #163, #160

0.3.0 (September 06, 2023)

Compare with 0.2.0

Enhancements, new features, and additions

• Replace unicode symbols with octicons/fontawesome icons (675e1ff by Oscar Esteban).
• Add ET description to intro (8bf5278 by Oscar Esteban). Related issues/PRs: #146, #153
• Deep revision of the PR (1fefe2d by Oscar Esteban).
• Added a safety check for the desiccant chamber color (7c13efc by Alexandre Cionca).

Bug Fixes

• Scanner name leak (71a5e81 by Alexandre Cionca).
• Indentation for rendering / show admonition folded (0747ffe by Oscar Esteban).
• Typos (ae572d9 by Céline Provins).
• Add missing picture in emergency procedures section (e977607 by Oscar Esteban). Related issues/PRs: #89

0.2.0 (August 29, 2023)

Compare with 0.1.0

Enhancements, new features, and additions

• Change icon of quote admonitions (fbadaed by Oscar Esteban).
• Large overhaul, including initial flowchart of the experiment (0e0d390 by Oscar Esteban).
• Add explanation in SOPs and code to run defacing (2d8982c by Céline Provins ).
• Add codespell (61717da by Oscar Esteban).
• Add folder structure of the BIDS dataset (c3d0a2a by Oscar Esteban). Related issues/PRs: #94
• Add tape for head motion (2dbae4d by Oscar Esteban). Related issues/PRs: #87
• Add STP100D and MMBT-S manuals (9feb336 by Oscar Esteban).
• Improve some admonitions (de3f034 by Oscar Esteban).

Bug Fixes

• Stop leaking host name (5a42d85 by Oscar Esteban). Related issues/PRs: #122
• Refactor of the preliminary section, separating an intro from it (19b4571 by Oscar Esteban).
• Trim trailing spaces, change admonition type (6e16e80 by Oscar Esteban).
• Revert removal of indentation in script file (9be8d05 by Oscar Esteban).
• Reorder some incongruent steps, move sound, light and ventilation (e1f4b4b by Oscar Esteban).
• Use octicons and fontawesome (09927cc by Oscar Esteban).
• Inconsistencies in the ET's eye-coverage setting and calibration (15cebe2 by Oscar Esteban).
• Misplaced ET description and minor revisions (60475e7 by Oscar Esteban). Related issues/PRs: #99
• Spell check and indentation with spaces (2c2cdeb by Oscar Esteban).
• Add a note regarding disruption on BIDS names after session 14 (1da4810 by Oscar Esteban).
• Wrong number of sessions at index page (1adb77d by Oscar Esteban).
• Typo (abe827c by Oscar Esteban).
• Improve the key listening (ead2438 by Oscar Esteban).

Maintenance and Continuous Integration

• Update git-changelog config (29d79f0 by Oscar Esteban).
• Fix file path and run black for style (164d8f1 by Oscar Esteban).

0.1.0 (June 29, 2023)

The first release of these SOPs. Currently, the document is still a work in progress, with the Data management, Preprocessing, and Release of data yet to be written.

Compare with first commit

Enhancements, new features, and additions

• Rename study-settings file (f53526e by Oscar Esteban).
• Add task timings and references (b21c717 by Oscar Esteban). Related issues/PRs: #73 Co-authored-by: Elodie Savary
• Add phys2bids commandline (0d22fd7 by Oscar Esteban).
• Change theme, add chuv logo, update data-storage (a00e833 by Oscar Esteban).
• Refining the participant preparation (f450fd2 by Oscar Esteban).
• Sectioning the participant preparation (84a4ee1 by Oscar Esteban).
• Revise @celprov's code (a011894 by Oscar Esteban).
• Minimal, stylistic changes (030a9ca by Oscar Esteban).
• Remove comment about starting recordings as it is now covered by #71 (e4fa2cf by Oscar Esteban).
• Overhaul of the scanning section of the SOPs (732c963 by Oscar Esteban).
• Add emergency procedures (fc52766 by Céline Provins ).
• Miscalleneous improvements and picture addition (b9b74c0 by Céline Provins ).
• Add info on how to configure the Acknowledge software and record physiolocal signals (f321875 by Céline Provins ).
• Add information about the outputs of the different sequences to better explain the procedure (c7db90a by Hélène Lajous).
• Add info about cleaning procedure (f15155a by Hélène Lajous).
• Correct typos and add info in case you know which exam will be run next (3d82aee by Hélène Lajous).
• Add details about how to switch to advanced user mode to save a protocol (8e5c46a by Hélène Lajous).
• Add details and correct a few typos (fdd742d by Hélène Lajous).
• Review comments (1745329 by Oscar Esteban).
• Add picture of the ET attached (eaa3a8a by Oscar Esteban).
• Setup mkpdfs plugin (2d6f9fd by Oscar Esteban).
• Make it louder (6d6cce4 by Oscar Esteban).
• Add info box about moving the mirror slightly to the right (589fd63 by Oscar Esteban).
• Add warning about attachment of infrared mirror (00c214d by Oscar Esteban).
• Miscalleneous improvements and image additions (a74aa6d by Céline Provins ).
• Give instructions on how to switch on the scanner (c83ad23 by Hélène Lajous).
• Improve how the scanner is switched off (f95d559 by Hélène Lajous).
• Say you want to turn the key (85180b4 by Hélène Lajous).
• [heudiconv heuristic] Do not deduplicate if run is found (5f15cca by Oscar Esteban).
• Add phone call script (8b10d1c by Céline Provins ).
• Add what to do if the alarm rings (f89e399 by Céline Provins ).
• Replace BIOPAC setup photo with Ines' annotated one (8e97af7 by Céline Provins ).
• Add missing bibliography (a667955 by Céline Provins ).
• Addition of miscalleneous information and of many missing pictures (20ad2bd by Céline Provins ).
• Add link to reproin (dd4978f by Oscar Esteban).
• Add a filter to show missing secrets as REDACTED or replace values (61451c8 by Oscar Esteban).
• Improvements to the data management section (2a176c1 by Oscar Esteban).
• Minimal improvements to clean-up (d20edf3 by Oscar Esteban).
• Add pictures and improve new exam description (c02291f by Oscar Esteban).
• Split data collection (516c388 by Oscar Esteban).
• Add GA video (944a525 by Oscar Esteban).
• Reorder misplaced steps, improve rendering (3ede838 by Oscar Esteban).
• Ensuring it looks good when rendered (07b0f04 by Oscar Esteban).
• Added some files, restructure and fix some items (3fa2c85 by Oscar Esteban).
• Fix typos and overhaul of data collection (00e3daf by Oscar Esteban).
• Add images of gas analyzer (6032ed0 by Céline Provins ).
• Add info how to setup the respiration belt and the gas analyzer (62bf6fd by Céline Provins ).
• Add info to setup BIOPAC (3719eca by Céline Provins ).
• Add info to turn off computer (3e66ec8 by Céline Provins ).
• Add info about plugging the coil after the exam has been open (1d5b501 by Céline Provins ).
• Add info about how to save the magnitude image of the fmap (d3efc7d by Céline Provins ).
• Add ack, edit/reorder some sections (46e41fa by Oscar Esteban).
• First pass at data collection checklist (2ab93f7 by Oscar Esteban).
• Update README (3833e37 by Oscar Esteban).

Bug Fixes

• Add missing settings file (0d4d3f8 by Oscar Esteban).
• [heudiconv heuristic] Identify phase and mag in func and fmap-epi (e1e3170 by Oscar Esteban).
• [heudiconv heuristic] Robuster detection of phase/mag in GRE fieldmaps (e65f0d2 by Oscar Esteban).
• Wrong path of mathjax (731dfdd by Oscar Esteban).
• Reorder scanning protocol to match sequences order in the manuscript (80ee8f4 by Céline Provins ).
• Correct console parameter name for reconstruction (dd1f3cf by Céline Provins ).
• Fix layout (3facec9 by Céline Provins ).
• Wrong link to psychopy git repo (33ed5e5 by Céline Provins ).
• Missing picture (7eb7f42 by Céline Provins ).
• Update RR figure 1 (387722b by Oscar Esteban).
• Add missing dependency (976ae4c by Oscar Esteban).
• Correct errors I introduced in @helenelajous' PR (3b656f2 by Oscar Esteban).
• [heudiconv heuristic] More sensible decision for phasediff fieldmaps (3d9b73e by Oscar Esteban).
• [heudiconv heuristic] Set run when duplicates of a sequence are found (504e217 by Oscar Esteban).
• [heudiconv heuristic] Overhaul of the reproin heuristic (6576b32 by Oscar Esteban).
• Minimal amends (9e9d56f by Oscar Esteban).
• PACSMAN instructions (b562372 by Oscar Esteban).
• PACSMAN csv file example (e0a8f66 by Oscar Esteban).
• Images with wrong paths, and names (5260d62 by Oscar Esteban).
• Miscellaneous stuff (df5a300 by Oscar Esteban).
• Update version of gha/checkout and fix path second time (cfcc19c by Oscar Esteban).
• Still setting up path (dfe542c by Oscar Esteban).
• Roll-back the path option (ac2661f by Oscar Esteban).
• Checkout action (1a149b2 by Oscar Esteban).
• Remove toc plugin (3861174 by Oscar Esteban).

Maintenance and Continuous Integration

• Set --in-place editing of the changelog (48f8acd by Oscar Esteban).
• Refine changelog update with git-changelog (e4ea298 by Oscar Esteban).
• Use git-changelog to update the changelog (856e58a by Oscar Esteban).
• Remove old exemplary code (2e5697c by Oscar Esteban).