Investigating non-default tracts via pyAFQ using a QSIrecon container pipeline

Software Support
1

Hello,

I am currently preparing a pipeline to process MRI data to look at DTI images of the fornix and do analysis. As part of this pipeline I plan to run QSIprep (1.0.0rc1) and QSIrecon (1.0.0rc2) to view the tactometry via pyAFQ. QSIrecon will be run as a container (apptainer), but by default the ouput from my testing do not include certain tracts like the fornix that I am interested in.
An answer to a previous similar question (pyAFQ Cingulum Outputs) refers to using pyafq templates including waypoint ROIs and probabilistic map for the HCC to look at the fornix, but I cannot find any instructions how to pass them to the container. Solutions along this manual(How to add new bundles into pyAFQ (Acoustic Radiations Example) — AFQ 1.3.2 documentation) recommend passing them as a bundleDict object… which I reckon would be done in the pyafq_tractometry.yaml file available on the github under the Bundle_info or presegment_bundle_dict.
An example would be greatly appreciated!
Thanks!

2

Hello - unfortunately, not all of the options available through pyAFQ are supported through QSIrecon, so you’d probably have to write some Python scripts (e.g., based on the online how-to examples) to perform this particular operation.