registration T2 with FA

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registration T2 with FA

gabriele pasqua


We want to extract FA values from MRI of spinal cord using 3dSlicer v4.5

In order to do this, this is the pipeline we used:

1)   conversion of T2 and dwi from DICOM to NRRD

2)   Filtering of DWI using DWI Joint Rician LMME filter with default parameters (estimation radius 2,2,1 and filtering radius 2,2,1)

3)   Diffusion Weighted masking  volume masking setting filtered DWI as input volume and Otsu Omega Threshold parameter set to 0,2 (please see image1)

4)   DWI to DTI Estimation, using filtered DWI as input, created mask as mask and WLS as estimation algorithm

5)   Diffusion tensor Scalar Measurements with which we computed FA from DTI

6)   2 times General Registration  using as fixed image T2 and as moving image FA. We used the following parameters:  Percentage of Samples (0,2), Bspline Grid Size (3,3,3) and Registration Phases Bspline (>27 DOF)

7)   Make ROI of spinal cord using Editor module (please see image2)


We got a good registration between T2 and FA, but we aspect to have a lower value of FA where we have a compression of spinal cord (please see image3), compared with results we got with GE software of MRI machine.


We got a mean value of 0,65 with 3dSlicer compared with 0,3 we got with GE software.


Maybe we’re wrong with some step of our pipeline.


Can you help us?


Thanks for your collaboration,


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