Change History

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

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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).