2025/11/11 (notes)

--- tags: TechMon --- # 2025/11/11 (notes) :::info - **Date:** November 11, 2025 - 12 pm EST - **Participants:** CM, EM, TS, OE, JHL ::: :::success ## Agenda 1. SBRefs/BOLDrefs failed INU correction: * https://neurostars.org/t/inconsistent-image-intensity-in-the-averaged-fmri-images-for-coregistrations-across-runs/34486 * Potentially duplicates [nipreps/fmriprep#3163](https://github.com/nipreps/fmriprep/issues/3163) 1. Templateflow S3 remote mess * https://github.com/templateflow/templateflow/issues/186 1. NiPreps .github repository content * License: license here is not Apache [https://github.com/nipreps/.github](https://github.com/nipreps/.github/blob/main/LICENSE) * CoC: Having a CoC there may avoid the need for all repositories to have a boilerplate CoC file. Avoid inconsistencies: https://github.com/nipreps/nifreeze?tab=coc-ov-file#readme, https://github.com/nipreps/dmriprep/blob/master/CODE_OF_CONDUCT.md * https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/creating-a-default-community-health-file 1. ITK has added [a markdown file](https://github.com/InsightSoftwareConsortium/ITK/pull/5607) to the repository following https://agents.md/. First PR asked to Copilot has not been good enough. Related resources: https://docs.github.com/en/copilot/concepts/agents/coding-agent/about-custom-agents, https://github.blog/changelog/2025-10-28-custom-agents-for-github-copilot/, https://github.com/github/awesome-copilot 1. NiPreps' Chart update including *PETPrep* * https://www.nipreps.org/ * (still needs revision of the BIDS' logo) ::: ## Meeting (automatic) summary ### Quick recap The team discussed technical issues with image processing tasks and registration problems, with plans to troubleshoot through visual examination and follow-up with external teams. They addressed concerns about template flow downloads and GitHub repository licensing, including the need for consistent master copies of licenses and code of conduct across projects. The conversation ended with discussions about visual assets and logos, emphasizing the importance of consolidating resources in the identity repository. ### Next steps * Oscar: Keep an eye on the reports from Japan regarding the image processing issue, and possibly request data sharing if no issues are found. * Chris: Work through template flow repositories to systematically remove S3 remotes not corresponding to the current template, build a script/process for this, and rerun export on all templates; document progress in the relevant issue. * Oscar: Follow up with Chris on the S3 remotes issue and review the process/notes after Chris completes the work. * Team (implied Oscar/Chris/Jon): Decide on a single code of conduct to use across all NiPreps repositories and consider moving it to the organization level for inheritance, possibly via the NSC for proposal/validation. * Oscar: Investigate why the Beats logo (SVG) is not showing in the project plot and resolve the issue. * Taylor: Add ASL Prep to the NiPreps project plot if desired. * Oscar: Continue migrating flowcharts and logos to the identity repository to avoid versioning issues and improve resource management. * Oscar: Test using an agent .md file in NiPrease or a small project to evaluate its usefulness for guiding AI contributions. ### Summary #### (Pre-meeting) Image Processing Quality Issues Discussion Jon and Oscar discussed issues with an image processing task, noting that the quality seemed compromised, possibly due to environmental changes or a mask being used instead of the full image. They agreed to try generating artifacts and examining the images visually to troubleshoot. Chris mentioned that Matías was out until December 5th and had not been active on Slack, so Oscar confirmed that Matías was indeed unavailable. #### 1. Image Registration Performance Issues Oscar discussed an issue reported by a Japanese contact regarding image registration problems, which appears to be related to N4's performance with certain Siemens scans. Chris clarified that "desk co-reg" refers to different bold references for head motion correction and co-registration, and Taylor mentioned that pre-scan normalization can sometimes affect ASL and QSI images, though this appears to be a different issue. Oscar agreed to monitor the situation and follow up with the Japanese team, while Chris suggested checking if this is a known issue in the ANTS mailing list. #### 2. TemplateFlow Chris identified a problem where S3 remotes were being incorrectly copied into template directories, likely due to manual errors by Oscar in the past. They agreed that Oscar would follow up on Chris's work to remove unnecessary S3 remotes and rerun exports. #### 3. Licensing, CoC & `nipreps/.github` repo Jon and Oscar discussed the need for a consistent master copy of licenses and code of conduct across projects. Oscar explained that while there is documentation about licenses, there isn't a specific excerpt to copy for projects. They agreed that a robot was planned to watch for changes in the governance repo or .github and propagate them across all projects, but this hasn't been implemented yet. Chris suggested using the .github directory as a single source of truth for the code of conduct, which Jon noted is currently a link to an old contributor covenant. Chris investigated that new repositories don't automatically inherit license information, and the team clarified that their documentation should be under CC0 while code repositories remain under Apache license. ##### Code of Conduct Implementation Review The team discussed the Code of Conduct for their projects, noting its automatic inheritance across repositories under the Insight Software Consortium. Jon explained that Matt had manually added a `CONTRIBUTING.md` file to the ITK repository to guide agents in contributing code, though its effectiveness was still being evaluated. Oscar suggested moving the Code of Conduct to the NSC for review and validation, while also considering testing the agent guidelines on a small project within NiPreps. #### 4. `AGENTS.md` Jon introduced the idea of agents files and described how Matt McCormick had been trialing it out within ITK. Oscar will test it with NiFreeze or one of those (smaller) of our projects. #### 5. Logo Consolidation and Display Issues Oscar discussed the status of logos and visual assets, noting that the BIDS logo was having issues displaying SVG files, and mentioned that Martin had approved the PETPrep logo. Oscar emphasized the importance of consolidating resources in the identity repository to avoid version discrepancies across different repositories. The conversation ended with Oscar mentioning the next meeting in two weeks.