Projects:RegistrationLibrary:RegLib C46

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v3.6.1 Slicer Registration Library Case #46: 2D Cine MRI of Breathing Cycle

Input

		this is the time series of 2D images to be registered with the reference
fixed image/target		moving image

Modules

• Slicer 3.6.1 recommended modules: BrainsFit

Objective / Background

We seek to study the motion of the lung during a breathing cycle by co-registering all of the images in a sequence with a reference, and then extract the motion from the registration displacement field.

Keywords

MRI, lung, 2D, time-series, deformation

Input Data

• reference/fixed : 2D coronal MRI 256x256
• moving: 2D coronal time series, 200 images total, each 256x256

Overall Strategy

1. select one frame within the breathing cycle as reference frame
2. compute non-rigid BSpline registration of all images to the reference frame
3. extract the displacements of indiv. grid nodes and plot over time

Procedures

• Phase I: Pilot to determine optimal registration parameters

1. load reference image and one moving image from the series
2. open Registration : BrainsFit module
   1. Registration Phases:
   2. set "reference" fixed and "moving_??" as moving image
      1. select/check Include BSpline registration phase
   3. Output Settings:
      1. select a new transform "Slicer BSpline Transform", rename to "Xf1_moving_??"
      2. select a new volume "Output Image Volume, rename to "moving_??_Xf1"
   4. Registration Parameters: increase Number Of Samples to 200,000
   5. Registration Parameters: set Number Of Grid Subdivisions to 5,5,5
   6. Leave all other settings at default
   7. click: Apply; (runtime < 10 sec. on MacPro)
   8. adjust grid size until registration is acceptable

• Phase II: Batch Run

1. open a terminal window
   1. via a TextEditor or prototyping/scripting software (e.g. Matlab), copy and modify the prototype line below, by changing only the moving input image:

 /Applications/Slicer36/Slicer3 --launch  /Applications/Slicer36/lib/Slicer3/Plugins/BRAINSFit --useBSpline --splineGridSize 5,5,5 --outputVolumePixelType short /
 --numberOfSamples 200000 --costMetric MMI --fixedVolume Reference/refLung_001.dcm --movingVolume Moving/Moving_001/Moving_001.dcm /
 --bsplineTransform Xforms/Moving_001_XfBSpl5.tfm --outputVolume MovingResampled/Moving_001_r.nrrd >> Logs/Moving_001_RegLog.txt 2>&1

1. 1. replace "/Applications/Slicer36" with your path of 3DSlicer
   2. create result directories MovingResampled, Logs, Xforms
   3. note that because input image is DICOM, and images are 2D only, each image of the time series must be in its own directory, otherwise Slicer will read them as a volume.
   4. paste all commands into a terminal window, or copy into a shell script and execute.
   5. upon completion, read the transform files with an editor and extract the displacements of interest

Registration Results

moving input File:RegLib C46 Displacements.pdf

Download

• Data
  • RegLib_C33_Data DWI, DTI, T1, FLAIR, Presets & solution transforms (NRRD files, zip file 174 MB)
  • RegLib_C33_Data_noDWI subset of the above, contains DTI but w/o DWI and resampled DTI (NRRD files, zip file 86 MB)
  • RegLib_C33_Data Transforms & Presets only contains only result transforms and parameter presets (NRRD files, zip file 30 kB)
• Presets
  • RegLib_C33_Presets Presets for FLAIR and DTI registration & DTI resampling (.mrml file 12 kB)
  • Link to User Guide: How to Load/Save Registration Parameter Presets

Discussion: Registration Challenges

• The DTI contains acquisition-related distortions (commonly EPI acquisitions) that can make automated registration difficult.

Acknowledgments

This case is the same data as case 40 from the fMRI neurosurgery data set on central.xnat.org