Howto retrorecon data_siemens
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This document provides steps to retrospectively reconstruct a dataset with different image processing options using a technique called RetroRecon. The key steps are: 1. Acquire a full dataset with one processing option and partial datasets with other options for comparison. 2. Open the full dataset in Twix and use RetroRecon to edit the XML file, pasting in the text from one of the partial dataset XML files to apply a different reconstruction. 3. Run the retrospective reconstruction to produce a new dataset with an _RR suffix using the alternate processing on the full dataset. This allows comparison of different reconstructions without other variability.
Howto retrorecon data_siemens
- 1. How to RetroRecon data with different ICE processing streams Erik Beall Cleveland Clinic August 9th, 2011
- 2. • Data may be reconstructed many ways • Re-acquiring data with different reco options introduces additional variability • The best solution is to reconstruct one raw dataset with alternate processing steps • This is possible with RetroRecon and XBuilder by hand-changing a few values – This is finicky and doesn’t always work • However, to get most out of it, we can trick RetroRecon into using FULL xml file…
- 3. Example: partial Fourier • We have some ep2d_diff data, but want to explore different partial Fourier reconstruction options: zero-filling, submatrix (we discover this is same as zero-filling), Margosian, and POCS. • We modified ep2d_diff to select any of these four partial Fourier reconstructions • But, we want to explore these on same data to remove any variability!
- 4. Preparation Steps • Acquire one full dataset (79 directions, 2mm iso DTI, b=1000, 52 axial slices) with any partial Fourier option selected • Next, acquire exact same scan, but with different partial Fourier option selected. Abort after first full volume is stored (use online display to be sure scan has run long enough to generate xml file). – This can be done on phantom, but make certain same slice prescription, table location, etc are used. ANY changes can alter processing – We have acquired one full scan and three partial scans with each pF option selected
- 5. Step 1: Open Twix Select dataset acquired with alternate reconstruction in left column Note, here is the original, zero-fill reconstruction, with all 79 dirs acquired. We will be applying the alternate reconstruction to this full dataset
- 6. Step 2: Run RetroRecon Click on RetroRecon button Click on “Edit” button, this will open xml in XBuilder
- 7. Step 3: “Edit” protocol Click on xml button, this will open the xml file in notepad
- 8. Step 3: Save alternate xml file Save this xml file somewhere and close notepad and XBuilder
- 9. Step 3: Select raw original dataset Now, select dataset acquired with original reconstruction in left column Click on RetroRecon, “Edit” and then xml file in XBuilder
- 10. Step 3: Open original xml file This is the original xml file. Ctl-A will highlight all text. Delete everything (note temp filename).
- 11. Step 3: Copy alternate xml text Open the saved alternate xml file, Ctrl-A to highlight everything, then Ctl-C to “copy” all alternate reconstruction text
- 12. Step 3: Paste alternate into original Go back to original xml notepad window and click Ctl-V (or paste) to paste all alternate xml text into the original xml file. Save using File->Save. Close all notepad windows and XBuilder
- 13. Step 3: Run Alternate Recon Click on “Start”. Wait.
- 14. Step 3: Done Done.
- 15. Step 3: data is in patient database Produces a scan with same name as the alternate reconstruction, but with _RR suffix
- 16. Caveats • I’ve tried to modify one xml file and use it on another dataset – this is really tricky. The scanner fills in a lot of entries that are difficult to get exactly correct. The only way to be sure is to regenerate the xml using a nearly-exact copy of the same scan, with identical slice and other prescriptions as in the full dataset and modify only the postprocessing options you desire (as in this howto).