DTI: Group Analysis Pipeline

Converting Dicom files into NRRD format

The conversion of DICOM images into NRRD format is done with the Slicer3 plugin tool DicomToNrrdConverter. This is included within the DTIPrep for convenience. This program should handle most images from GE and Siemens scanners including Mosaic format images. For Siemens scanners, software version above VB13 should be supported. We would like to thank Xiaodong Tao for his great work on this tool. This program should read the diffusion directions from the DICOM header.

 % DicomToNrrdConverter <DICOM-Directory> <OutputDirectory> <OutputFilename>

The output file will contain the Diffusion weighted images in a vector format. The DTI analysis pipeline within NIRAL expects the DWI/DTI in NRRD format. Try to use the DicomToNrrdConverter after Jan 2009 to avoid a bug in the old version.

DWI/DTI Quality control (QC)

Diffusion Information checking

DWI cropping/padding

DTI computing

• dtiestim
• dtiprocess

Integrated tool: DTIPrep

DTIPrep is a locally developed tool for DWI/DTI quality control and preparation.It is both a GUI and command line tool, enabling users to do QC either in a manual/visual way or in an automatic way. Use it in a script will enable an automatic batch processing for population data processing.

1. Using in GUI mode
   • Working with DWI files
     • Load a NRRD DWI file

Currently, DTIPrep can only load NRRD format DWI files. Load an NRRD DWI through the File menu of by clicking the load NRRD tool button in the tool bar.

1. • Working with protocol files
     • Load an existing xml protocol file
     • Create a protocol and save it
   • Working with QC files
     • manually check
     • Protocol based check
2. Using in command line

  DTIPrep --help
  Command tags: 
  -w --DWINrrdFile < DWIFileName > 
     = DWI file name to convert dicom image series into or to be checked (nhdr)
  [ -d --DicomDirectory < InputDicomDir > ]
     = Directory containing dicom images to be converted
  [ -p --xmlProtocol < xmlFileName > ]
     = protocol xml file
  [ -n --resultNotesFile < NotesFile > ]
     = result notes
  [ -f --outputFolder < OutputFolder > ]
     = output folder name

Analysis

ROI based analysis

 NRRD0005

Voxel-wise analysis

 NRRD0005

Along-tract analysis

Fiber tracking in atlas

• Slicer

Cleaning the fiber tracks

• FiberViewer

Extracting fiber tracts in all the individuals

• fiberprocess

Extracting along-tract diffusion properties

• FiberViewer

---

--Zhliu 20:05, 6 August 2009 (UTC)zhliu