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| @@ -1,4 +1,5 @@ | ||
| Céline Provins <[email protected]> | ||
| Céline Provins <[email protected]> cprovins | ||
| Céline Provins <[email protected]> celprov | ||
| Céline Provins <[email protected]> <[email protected]> | ||
| Elodie Savary <[email protected]> | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| | Version | Date | Description / comments | By | | ||
| |-----------|------------|------------------------|-----------| | ||
| | 22.0.0 | 2022-02-21 | Initial draft | @oesteban | | ||
| All notable changes to these SOPs are documented below, starting with the most recent version of the document. | ||
|
|
||
| !!! note "You found an error" | ||
|
|
||
| If you want to check the list of open issues, please proceed to our [issue tracker](https://github.com/TheAxonLab/hcph-protocol/issues). | ||
|
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||
| 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](https://github.com/TheAxonLab/hcph-protocol/issues/new). | ||
|
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||
| <!-- insertion marker --> | ||
| ## [0.1.0](https://github.com/TheAxonLab/hcph-protocol/releases/tag/0.1.0) (June 29, 2023) | ||
|
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||
| The first release of these SOPs. | ||
| Currently, the document is still a work in progress, with the [Data management](data-management/post-session.md), [Preprocessing](preprocessing.md), and [Release of data](release.md) yet to be written. | ||
|
|
||
| <small>[Compare with first commit](https://github.com/TheAxonLab/hcph-protocol/compare/51fbd53f255aa8ee25b1ecb38b3429c400fabea3...0.1.0)</small> | ||
|
|
||
| ### Enhancements, new features, and additions | ||
|
|
||
| - Rename study-settings file | ||
| ([f53526e](https://github.com/TheAxonLab/hcph-protocol/commit/f53526ecec5cbe26679f8bbcfea134306571cde7) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add task timings and references | ||
| ([b21c717](https://github.com/TheAxonLab/hcph-protocol/commit/b21c7171139a4a19060fc648e41cf1dc019a05e7) by [Oscar Esteban](https://github.com/oesteban)). Related issues/PRs: [#73](https://github.com/TheAxonLab/hcph-protocol/issues/73) Co-authored-by: [Elodie Savary](https://github.com/esavary) | ||
| - Add *phys2bids* commandline | ||
| ([0d22fd7](https://github.com/TheAxonLab/hcph-protocol/commit/0d22fd71d28f59c405b5f01fab18127780be6ea2) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Change theme, add chuv logo, update data-storage | ||
| ([a00e833](https://github.com/TheAxonLab/hcph-protocol/commit/a00e83325f02110c0c1a7a3389def10339475115) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Refining the participant preparation | ||
| ([f450fd2](https://github.com/TheAxonLab/hcph-protocol/commit/f450fd208ceb83fa0c800be6e71e6231c2a0a25a) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Sectioning the participant preparation | ||
| ([84a4ee1](https://github.com/TheAxonLab/hcph-protocol/commit/84a4ee1b6a306fafda8e7c7332db423003986d0b) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Revise [@celprov](https://github.com/celprov)'s code | ||
| ([a011894](https://github.com/TheAxonLab/hcph-protocol/commit/a0118947eb563bfdc6e329d73a82abe7702c76c2) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Minimal, stylistic changes | ||
| ([030a9ca](https://github.com/TheAxonLab/hcph-protocol/commit/030a9caf7c422e117a4fb4b9f339fa1be7c08d68) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Remove comment about starting recordings as it is now covered by [#71](https://github.com/TheAxonLab/hcph-protocol/issues/71) | ||
| ([e4fa2cf](https://github.com/TheAxonLab/hcph-protocol/commit/e4fa2cf301ad7b7b8a7f35ddc0a6bb37f412278e) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Overhaul of the scanning section of the SOPs | ||
| ([732c963](https://github.com/TheAxonLab/hcph-protocol/commit/732c9632d91a6f537af026227e178d10c48030c7) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add emergency procedures | ||
| ([fc52766](https://github.com/TheAxonLab/hcph-protocol/commit/fc52766e9793ad516155df01d54b57f27f1e94c1) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Miscalleneous improvements and picture addition | ||
| ([b9b74c0](https://github.com/TheAxonLab/hcph-protocol/commit/b9b74c05a5bc697bd8c43cd8513dcb0b057fde53) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add info on how to configure the Acknowledge software and record physiolocal signals | ||
| ([f321875](https://github.com/TheAxonLab/hcph-protocol/commit/f32187555b9a399b5cafab56530318bd29a38d84) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add information about the outputs of the different sequences to better explain the procedure | ||
| ([c7db90a](https://github.com/TheAxonLab/hcph-protocol/commit/c7db90a871620e7df2a0f0495e04e024b85936ce) by [Hélène Lajous](https://github.com/helenelajous)). | ||
| - Add info about cleaning procedure | ||
| ([f15155a](https://github.com/TheAxonLab/hcph-protocol/commit/f15155a5103b53c6f6526d6a9e07aca03f3b0388) by [Hélène Lajous](https://github.com/helenelajous)). | ||
| - Correct typos and add info in case you know which exam will be run next | ||
| ([3d82aee](https://github.com/TheAxonLab/hcph-protocol/commit/3d82aee5b703eb812e6c23ecd4bca84b05eb173f) by [Hélène Lajous](https://github.com/helenelajous)). | ||
| - Add details about how to switch to advanced user mode to save a protocol | ||
| ([8e5c46a](https://github.com/TheAxonLab/hcph-protocol/commit/8e5c46a02ea0f725b3e2404329b3428ce31df3a7) by [Hélène Lajous](https://github.com/helenelajous)). | ||
| - Add details and correct a few typos | ||
| ([fdd742d](https://github.com/TheAxonLab/hcph-protocol/commit/fdd742de2266e0ab2e7aa76252619c52c207c200) by [Hélène Lajous](https://github.com/helenelajous)). | ||
| - Review comments | ||
| ([1745329](https://github.com/TheAxonLab/hcph-protocol/commit/1745329924878c5dc81b6b7d1697b93029a1f61b) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add picture of the ET attached | ||
| ([eaa3a8a](https://github.com/TheAxonLab/hcph-protocol/commit/eaa3a8a3b7b8a9f6e18ef1b5b469ab04de516fee) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Setup *mkpdfs* plugin | ||
| ([2d6f9fd](https://github.com/TheAxonLab/hcph-protocol/commit/2d6f9fd1d7819943adb0312bf397945a0be5ac19) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Make it louder | ||
| ([6d6cce4](https://github.com/TheAxonLab/hcph-protocol/commit/6d6cce44cfcd39b00af88617c45a9bebd48050d3) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add info box about moving the mirror slightly to the right | ||
| ([589fd63](https://github.com/TheAxonLab/hcph-protocol/commit/589fd6387dc4c6a35b1a0ec94cbd57c8d3400297) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add warning about attachment of infrared mirror | ||
| ([00c214d](https://github.com/TheAxonLab/hcph-protocol/commit/00c214d26232700293199788b40615422ddab683) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Miscalleneous improvements and image additions | ||
| ([a74aa6d](https://github.com/TheAxonLab/hcph-protocol/commit/a74aa6d4989b3bcf600086140fa79788ca53b6cb) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Give instructions on how to switch on the scanner | ||
| ([c83ad23](https://github.com/TheAxonLab/hcph-protocol/commit/c83ad232a763e7aaf7ce427f1ceb98d6d4a3b29e) by [Hélène Lajous](https://github.com/helenelajous)). | ||
| - Improve how the scanner is switched off | ||
| ([f95d559](https://github.com/TheAxonLab/hcph-protocol/commit/f95d55990c4106d8e6b19b2bf0693ab7536830b7) by [Hélène Lajous](https://github.com/helenelajous)). | ||
| - Say you want to turn the key | ||
| ([85180b4](https://github.com/TheAxonLab/hcph-protocol/commit/85180b44d3b0d825e245cb3baac8e3da1d9703de) by [Hélène Lajous](https://github.com/helenelajous)). | ||
| - [heudiconv heuristic] Do not deduplicate if run is found | ||
| ([5f15cca](https://github.com/TheAxonLab/hcph-protocol/commit/5f15ccaf59aa974b56a98de2b94be571e4562e15) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add phone call script | ||
| ([8b10d1c](https://github.com/TheAxonLab/hcph-protocol/commit/8b10d1c96cb8fd1e0bb3a3233e53e329f2443584) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add what to do if the alarm rings | ||
| ([f89e399](https://github.com/TheAxonLab/hcph-protocol/commit/f89e39977e01aa39866742c66b3ff473182dd586) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Replace BIOPAC setup photo with Ines' annotated one | ||
| ([8e97af7](https://github.com/TheAxonLab/hcph-protocol/commit/8e97af771d0bf7758cf86468d551248e5f8e0d14) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add missing bibliography | ||
| ([a667955](https://github.com/TheAxonLab/hcph-protocol/commit/a6679559e1f7a604ffda222c73bd4062d04be9d2) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Addition of miscalleneous information and of many missing pictures | ||
| ([20ad2bd](https://github.com/TheAxonLab/hcph-protocol/commit/20ad2bd88603b6e84ca82e045fb9227d12fda17c) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add link to reproin | ||
| ([dd4978f](https://github.com/TheAxonLab/hcph-protocol/commit/dd4978f5bcc6aa323cbe1e97f5a2986c6760e042) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add a filter to show missing secrets as REDACTED or replace values | ||
| ([61451c8](https://github.com/TheAxonLab/hcph-protocol/commit/61451c847c3553d85c9c406f3df317400314ea69) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Improvements to the data management section | ||
| ([2a176c1](https://github.com/TheAxonLab/hcph-protocol/commit/2a176c15d3bba5fc06f177b4b42af7f011de8c2f) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Minimal improvements to clean-up | ||
| ([d20edf3](https://github.com/TheAxonLab/hcph-protocol/commit/d20edf3e87360d8dce1280c669edb6bc4559a3de) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add pictures and improve new exam description | ||
| ([c02291f](https://github.com/TheAxonLab/hcph-protocol/commit/c02291f82d784bfa006c101cb20bce8c913851df) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Split data collection | ||
| ([516c388](https://github.com/TheAxonLab/hcph-protocol/commit/516c388cb1a38c699eb381b2f0586b617e16b73b) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add GA video | ||
| ([944a525](https://github.com/TheAxonLab/hcph-protocol/commit/944a525880b2263f7c6b6b719fcf7f33f1fe4d3e) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Reorder misplaced steps, improve rendering | ||
| ([3ede838](https://github.com/TheAxonLab/hcph-protocol/commit/3ede838775d3437c4fe377e47cf34a4d7e2e38f3) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Ensuring it looks good when rendered | ||
| ([07b0f04](https://github.com/TheAxonLab/hcph-protocol/commit/07b0f04bf2298d818b97eb535885f9a4fe33ef02) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Added some files, restructure and fix some items | ||
| ([3fa2c85](https://github.com/TheAxonLab/hcph-protocol/commit/3fa2c85215c1881ed84cfa30c357f33847e84a07) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Fix typos and overhaul of data collection | ||
| ([00e3daf](https://github.com/TheAxonLab/hcph-protocol/commit/00e3daffd2c844e274f6902220c05263a169c878) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add images of gas analyzer | ||
| ([6032ed0](https://github.com/TheAxonLab/hcph-protocol/commit/6032ed01e4dfe354e8a2d3a59c6a6d5a957247f7) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add info how to setup the respiration belt and the gas analyzer | ||
| ([62bf6fd](https://github.com/TheAxonLab/hcph-protocol/commit/62bf6fd2c7ab4a26396834432c752ef4cd436775) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add info to setup BIOPAC | ||
| ([3719eca](https://github.com/TheAxonLab/hcph-protocol/commit/3719eca2529eaa681287c47edafc10f8a37b9850) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add info to turn off computer | ||
| ([3e66ec8](https://github.com/TheAxonLab/hcph-protocol/commit/3e66ec85861eab28338081da436aa0286a0fa9c8) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add info about plugging the coil after the exam has been open | ||
| ([1d5b501](https://github.com/TheAxonLab/hcph-protocol/commit/1d5b501d7fd31b85f796ea24c44e15dd772ba1ba) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add info about how to save the magnitude image of the fmap | ||
| ([d3efc7d](https://github.com/TheAxonLab/hcph-protocol/commit/d3efc7dc2b6eed9e5dd8662fe545d100102f66cb) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Add ack, edit/reorder some sections | ||
| ([46e41fa](https://github.com/TheAxonLab/hcph-protocol/commit/46e41fab015c6bd923a571f05fb69f916f9a10c2) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - First pass at data collection checklist | ||
| ([2ab93f7](https://github.com/TheAxonLab/hcph-protocol/commit/2ab93f7e3e908f66a28ec124500c57853cf82e37) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Update README | ||
| ([3833e37](https://github.com/TheAxonLab/hcph-protocol/commit/3833e370c8d15e8263e34ae66d3a530dec13a2d7) by [Oscar Esteban](https://github.com/oesteban)). | ||
|
|
||
| ### Bug Fixes | ||
|
|
||
| - Add missing settings file | ||
| ([0d4d3f8](https://github.com/TheAxonLab/hcph-protocol/commit/0d4d3f8ce7490657f0517595a71103996eb14615) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - [heudiconv heuristic] Identify phase and mag in func and fmap-epi | ||
| ([e1e3170](https://github.com/TheAxonLab/hcph-protocol/commit/e1e3170d8da31a55d1a7b7cf1b53d9d7ed953844) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - [heudiconv heuristic] Robuster detection of phase/mag in GRE fieldmaps | ||
| ([e65f0d2](https://github.com/TheAxonLab/hcph-protocol/commit/e65f0d2a6e26dcf3a96d21cce34d9febef727ec6) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Wrong path of mathjax | ||
| ([731dfdd](https://github.com/TheAxonLab/hcph-protocol/commit/731dfddd89f49ef5980e7c3da9b3ea77f84e9a14) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Reorder scanning protocol to match sequences order in the manuscript | ||
| ([80ee8f4](https://github.com/TheAxonLab/hcph-protocol/commit/80ee8f4002cdd9ed003e9296b11355a2b18582ed) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Correct console parameter name for reconstruction | ||
| ([dd1f3cf](https://github.com/TheAxonLab/hcph-protocol/commit/dd1f3cfff78eb02521b7d73d91a3dc1770eea75f) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Fix layout | ||
| ([3facec9](https://github.com/TheAxonLab/hcph-protocol/commit/3facec988c160ffda362e71df55e6840b886d273) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Wrong link to *psychopy* git repo | ||
| ([33ed5e5](https://github.com/TheAxonLab/hcph-protocol/commit/33ed5e5bc9610bb660f448550903e145da221389) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Missing picture | ||
| ([7eb7f42](https://github.com/TheAxonLab/hcph-protocol/commit/7eb7f42f37d064252f3ee2884d7d1017fc9db0ea) by [Céline Provins](https://github.com/celprov) | ||
| ). | ||
| - Update RR figure 1 | ||
| ([387722b](https://github.com/TheAxonLab/hcph-protocol/commit/387722b35f7e93a0f67b5dadd32468d2e7e62fa2) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Add missing dependency | ||
| ([976ae4c](https://github.com/TheAxonLab/hcph-protocol/commit/976ae4cc269e1d5b82d9dcebf2087912379de9d3) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Correct errors I introduced in [@helenelajous](https://github.com/helenelajous)' PR | ||
| ([3b656f2](https://github.com/TheAxonLab/hcph-protocol/commit/3b656f27fe6185b9e1af0c0fc84528895b748d91) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - [heudiconv heuristic] More sensible decision for phasediff fieldmaps | ||
| ([3d9b73e](https://github.com/TheAxonLab/hcph-protocol/commit/3d9b73e73f6fb4735eb73bfbde084cf1346e9e8a) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - [heudiconv heuristic] Set run when duplicates of a sequence are found | ||
| ([504e217](https://github.com/TheAxonLab/hcph-protocol/commit/504e2170dc92b607bcfd7d356d6bb5a02cb7f8ca) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - [heudiconv heuristic] Overhaul of the reproin heuristic | ||
| ([6576b32](https://github.com/TheAxonLab/hcph-protocol/commit/6576b321ec641c1eaea3e0800ea865a37ad8061a) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Minimal amends | ||
| ([9e9d56f](https://github.com/TheAxonLab/hcph-protocol/commit/9e9d56f6d8cb0318b3ed382a0e31381f762fb311) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - PACSMAN instructions | ||
| ([b562372](https://github.com/TheAxonLab/hcph-protocol/commit/b5623725f97e5832e1cb1bcb7da0c91c71cd5ed6) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - PACSMAN csv file example | ||
| ([e0a8f66](https://github.com/TheAxonLab/hcph-protocol/commit/e0a8f66725c2048235b7ea6a6357e5982890b53f) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Images with wrong paths, and names | ||
| ([5260d62](https://github.com/TheAxonLab/hcph-protocol/commit/5260d62d8f455e9ed285f3de233b39ffc6d2b91e) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Miscellaneous stuff | ||
| ([df5a300](https://github.com/TheAxonLab/hcph-protocol/commit/df5a300a4f84237ef0607c464b431cca0c3a16b7) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Update version of gha/checkout and fix path second time | ||
| ([cfcc19c](https://github.com/TheAxonLab/hcph-protocol/commit/cfcc19c1a8da01f6d07ef4a58b3ac2cbd3bd0383) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Still setting up path | ||
| ([dfe542c](https://github.com/TheAxonLab/hcph-protocol/commit/dfe542c96d3b1a064075715c5b7a09f98c29bc49) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Roll-back the path option | ||
| ([ac2661f](https://github.com/TheAxonLab/hcph-protocol/commit/ac2661f25f768e27a0b71c6145ca9de2a1fdf333) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Checkout action | ||
| ([1a149b2](https://github.com/TheAxonLab/hcph-protocol/commit/1a149b2207ea72118e82e2f664431b5b8185870c) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Remove toc plugin | ||
| ([3861174](https://github.com/TheAxonLab/hcph-protocol/commit/38611744407fe9101edce0dfca812b930c2fbaf5) by [Oscar Esteban](https://github.com/oesteban)). | ||
|
|
||
| ### Maintenance and Continuous Integration | ||
|
|
||
| - Set `--in-place` editing of the changelog | ||
| ([48f8acd](https://github.com/TheAxonLab/hcph-protocol/commit/48f8acdab772c69d4a7cf1305562958292b4c163) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Refine changelog update with *git-changelog* | ||
| ([e4ea298](https://github.com/TheAxonLab/hcph-protocol/commit/e4ea298cddd965c6e01953ded4f0868e4645899f) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Use *git-changelog* to update the changelog | ||
| ([856e58a](https://github.com/TheAxonLab/hcph-protocol/commit/856e58a56f14861ce1bce6d9079d26b9e63ca539) by [Oscar Esteban](https://github.com/oesteban)). | ||
| - Remove old exemplary code | ||
| ([2e5697c](https://github.com/TheAxonLab/hcph-protocol/commit/2e5697cb7c627422db6b5ffb2a71c017f84ef216) by [Oscar Esteban](https://github.com/oesteban)). | ||
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