Week of 5.8.23 to 5.12.23

• Freesurfer ingress + ABCD pipeline flow overhaul.
  • Over the past two weeks, the flow (but not the steps/methods) of the CPAC's abcd-options pipeline has been overhauled to be more in line with the original pipeline when users decide to ingress pre-computed Freesurfer outputs.
  • The ABCD pipeline has a "pre-Freesurfer step" which runs minimal preprocessing on the T1w data before it goes into Recon-All. The rest of the ABCD pipeline then continues with the Recon-All outputs.
  • Users now have the option to run a CPAC preconfig named "abcd-prep" which runs this pre-Freesurfer minimal preprocessing. Users can then take this data and run Freesurfer separately as they see fit. The results of this can then be ingressed back into CPAC with the abcd-options preconfig.
  • These changes have been tested extensively, and a container with these changes has been handed over to Nathalia so she could run a subset of the larger runs she will be performing with these features, as a sanity check.
• fmriprep ingress.
  • Although an original issue with ingressing multiple BOLD scans has been resolved, an issue with having the Nipype iterables work properly persists. We'll be parking that for now, and Elizabeth will be completing the last other part - ensuring the fmriprep confounds.tsv/regressors works nicely with our nuisance regression - starting Monday.
  • Once that is operational, we'll be able to safely dedicate all of our resources to the iterables issue without having any other outstanding to-do items hanging.
• Testing automation.
  • The automation of the CPAC runs for the regression test is complete. The next step is automating the generation of the correlation figures, which Amy is currently working on now.
  • The next step after this will be to include the QC figures in the automation such that we get automated data overlays and snapshots with every PR merge.
• fmriprep BOLD mask mapping.
  • Teresa has secured all of the intermediate data from the Anna/Leona data+runs and is currently mapping out the differences in the template-space BOLD mask generation between fmriprep and CPAC.
• Notch filter changes (via Alex Franco and Paul Bloom).
  • Elizabeth has taken on this project from Jon while Jon is on parental leave.
  • Elizabeth currently has the task to revert to a previous implementation of the filter which showed better results. However, this is currently parked as the fmriprep ingress is a higher priority.