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.