How to RetroRecon data with different ICE processing

streams

Erik Beall

Cleveland Clinic

August 9th, 2011

• 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…

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!

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

Step 1: Open Twix

Select dataset acquired withalternate reconstruction in left column

Note, here is the original, zero-fillreconstruction, with all 79 dirs acquired.

We will be applying the alternatereconstruction to this full dataset

Step 2: Run RetroRecon

Click on RetroRecon button

Click on “Edit” button,this will open xml in XBuilder

Step 3: “Edit” protocol

Click on xml button,this will open the xml

file in notepad

Step 3: Save alternate xml file

Save this xml file somewhere andclose notepad and XBuilder

Step 3: Select raw original dataset

Now, select dataset acquired withoriginal reconstruction in left column

Click on RetroRecon, “Edit”and then xml file in XBuilder

Step 3: Open original xml file

This is the original xml file.Ctl-A will highlight all text.Delete everything (note

temp filename).

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

Step 3: Paste alternate into original

Go back to original xml notepadwindow and click Ctl-V (or paste)to paste all alternate xml text into

the original xml file.Save using File->Save. Close allnotepad windows and XBuilder

Step 3: Run Alternate Recon

Click on “Start”. Wait.

Step 3: Done

Done.

Step 3: data is in patient database

Produces a scan with same nameas the alternate reconstruction, but

with _RR suffix

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).