---
# System prepended metadata

title: 2023/09/26 (minutes)
tags: [TechMon]

---

# Technical Monitoring (minutes) - 2023 September 26

:::info
**Date:** Sep 26, 2023 17:00(UTC)

**Agenda**: [link](https://hackmd.io/@NiPreps-technical-monitoring/rJqK12GEh)


**Participants:**
  - Chris (CM)
  - Celine (CP)
  - Ariel (AR)
  - Mathias (MG)
  - Eilidh (EM)
  - Oscar (OE)

 

**Minutes by:** ES
:::
### SDCflows PRs - Testing with fMRIPrep-minimal:
CM presented a new method for correcting susceptibility distortions. Currently, when working with phasediff images, the field estimate outside the mask is not used in creating the B-spline representation. This can result in substantial errors beyond the mask area, causing EPI signal distortion that extends far outside the brain and blurs the signal at the brain's edges.
The new method addresses this issue by allowing the use of an estimation mask during the correction process. The code is not part of an official release now but is available as a pull request (PR) against the master branch.

  * [#393](https://github.com/nipreps/sdcflows/pull/393) Rewrite of B-spline estimate using `scipy.interpolate.BSpline`. Restores optimizations lost in [#388](https://github.com/nipreps/sdcflows/pull/393) and uses a method that allows derivatives to be taken.
  * [#395](https://github.com/nipreps/sdcflows/pull/395) Enable masking the fieldmap during application to avoid spurious peaks outside brain
      * fMRIPrep paired PR: [#3094](https://github.com/nipreps/fmriprep/pull/3094)

### Drop in fMRIPrep for the last 2-3 weeks. From ~70% to ~50% success:
We've noticed a significant decrease in the performance of fMRIPrep recently. Normally, we achieve a success rate of around 70%, but now we're seeing a substantial increase in the number of failed runs. After checking on Century, the drop seems to be caused by a particular individual using an old version. 
### fMRIPrep-rodents: 
In a previous meeting, EM discussed the successful application of fMRIPrep-rodents to a large dataset. The code is now almost ready for testing and includes integration with SDCflow. You can access sample reports here for the next two weeks.
The primary challenge at the moment is brain masking in BOLD images. We should consider whether it's necessary to retain brain masking in this specific context or opt for the use of the anatomical brain mask instead. Further discussion on this matter is required.
### Per session visual reports
CP is working on a new workflow to create a visual report for every session. This workflow will separate anatomical images from fMRI data. In projects where a dedicated fieldmap for every session is not available, the fieldmap must be linked to the anatomical data.