DSI Studio

Reconstructing DWI

DSI Studio’s QSDR algorithm is very useful for reconstructing DWI data in a standard space. The process begins with creating a .src file

$ dsi_studio \
    --action=src \
    --source=/path/to/dicom_files \
    --output=output.src.gz

Once the .src.gz is created, reconstruct it with

$ dsi_studio \
    --action=rec \
    --thread=2 \
    --source=output.src.gz \
    --method=7 \
    --param0=1.25 \
    --param1-2 \
    --output_map=1

This will produce a map.fib.gz file.

Fiber Tracking

Tractography is performed on the map.fib.gz file. Supposing the goal is to reconstruct 100,000 streamlines with some conservative parameters. See DSI Studio’s documentation <http://dsi-studio.labsolver.org/Manual/Fiber-Tracking> to tune the parameters appropriately.

$ dsi_studio \
    --action=trk \
    --fiber_count=100000 \
    --turning_angle=55 \
    --min_length=10 \
    --smoothing=0.0 \
    --max_length=400 \
    --output=output.trk

These parameters work well for data from a Siemens Tim Trio 3T scaner. Your mileage may vary.