ImageAnalysisToolsManuals

Image Analysis Tools Info (feel free to add anything!)

General Purpose tools

• 3D Slicer
  • Slicer 4.3.1 is currently available on our system in /tools/Slicer4/Slicer-4.3.1-linux-amd64
  • Slicer 3.6.3 is still available on our system in /tools/Slicer3
  • General information about 3D Slicer usage on the wiki Slicer3 wiki page
  • Notes
    • You can write fiber .gipl into .vtk and load them into slicer3 for visualization

Segmentation tools

• InsightSnap
  • Insight Snap Webpage by Kitware
• Head circumference tool Manual

DTI tools

• dtiprocess
  • Usage: dtiprocess --dti_image tensor-image [options] (rotate,color mapping, warping etc)
  • tensor image .nrrd made by dtiestim
  • option for rotate: -r outputfile -d .dof file. .dof file made by rview
  • option for color mapping: -c
  • notes: non-finite elements for SVDC-need to be resoloved

• dtiestim
  • Usage: compute tensor image from DWIs
  • dtiestim --dwi_image dwi-image --tensor_output tensor-output [options]
  • e.g. dtiestim --dwi_image dwi_crop.nhdr --tensor_output tensors1.nrrd -t 200 --weight-iterations 1 -m lls

• rview
  • Image analysis tools developed by Daniel Rueckert & Julia Schnable at 2001
  • Visualization, Transformation and registration
  • Steps for rotate .gipl
    • Load FA files as source. click B, then ">" to multiply resolustion
    • In transformation, choose "rigid 3D"
    • Adjust x,y,z
    • Save file as .dof for futher use with dtiprocess

• fibertrack
  • Explore diffusion tensor images and to reconstruct fiber tracts
  • Usage: fibertrack [options]

• fiberviewer
  • Fiber Viewer is a program to analyze fibers extracted from the Fiber Tracking tool.
  • It provides:
    • Several methods for clustering
    • Tools for manipulate fibers
    • Methods to analyse FA and ADC along fibers
  • Notes
    • No mac version yet. For mac machine, you need view your fiber files in Slicer3

• convertITKformats
  • Convert formats including .nhrd .nrrd .gipl etc

• Steps of using fibertrack to compute fiber in fornix ROI
  • change the ROI format: gzip fornixROI.gipl, convertITKformats fornixROI.gipl.gz fornixROI.nrrd
  • fibertracking: you can set up parameters: fibertrack -i dti_crop.nhdr -r fornixROI.nrrd -o fornix.fib --step-size 0.039 --min-fa 0.15 --max-deviation 0.5
  • check the fiber file: more fornix.fib

• ImageMath: crop tools
  • Use InsightSNAP or MriWatcher to determine x,y,z,width,height,depth
  • Use ImageMath to crop, e.g. ImageMath b0_crop.nhdr-crop <x,y,z,width,height,depth> -outfile b0_crop2.nhdr
  • Copy the dwi_crop.nhdr to dwi_crop2.nhdr, and adapt it to reflect the change in name of the datafile, as well as the size change (check also the information in b0_crop2.nhdr)

• MriWatcher
  • MriWatcher is a vizualisation tool for MRI images. It uses coupled cursors to show the differences between images.

• Deft_dti
  • Deft_dti is a vizualisation tool for DTI images. It shows the tensors as glyphs (ellipsoids, superquadrics,...). It also shows the scalar measurements of the DTI.

• Slicer4 - See 'General Purpose Tools'