qsiplan
It’s a good idea to qsiplan before you qsiprep.
qsiplan plans and explains qsiprep’s diffusion-MRI preprocessing from BIDS metadata and configuration flags. It groups a subject’s DWI scans the way qsiprep will (distortion groups, fieldmap estimations, correction units, outputs), validates the data and curation (missing phase-encoding metadata, IntendedFor conflicts, shim inconsistencies, b-value mismatches), compiles the execution plan for any combination of head-motion and susceptibility-correction methods, and renders it all as text or as a self-contained interactive HTML page. Nothing is processed and nothing in the dataset is written.
Quickstart
pip install qsiplan
qsiplan /path/to/bids
qsiplan /path/to/bids --html grouping.html
The first command prints the grouping report and a processing preview for every default method combination. The second also writes an explorer page with live controls for every grouping and method flag.
- Installation
- Concepts
- Command line
- Issue codes
- Methods
- Understanding scan grouping
- 1. One scan, no metadata
- 2. A reverse phase-encoded partner appears
- 3. Curating fieldmaps:
B0FieldIdentifier/B0FieldSource - 4. Splitting outputs with
MultipartID— and borrowing - 5. Partial curation: curating some scans and not others
- 6.
ShimSetting: when the scanner re-shims - 7. No fieldmap at all: the anatomical SDC reference
- 8. Same grouping, different pipelines
- Appendix:
IntendedFor(deprecated) - Try it on your own data
- API reference
- Changelog
- Contributing