Fibre length measurements

njeffery · June 1, 2022, 6:47pm

Hi 3Dslicer community

Hoping someone has a solution out there. I have a vtk file with about 300 fibres in it. I need the length of each fibre. Seems a trivial task but I cannot find a solution.

Diffusion>quantify>tractography measurements will give the mean but there are lots of outliers, so its not representative. Need the median.

PS. I have tried the whitematteranalysis as well and cannot get it to work.

Do I need to use a different DTI package?

Any suggestions greatly appreciated.
cheers
NJ

Operating system:Windows 10
Slicer version:5.02
Expected behavior:
Actual behavior:

zhangfanmark · June 1, 2022, 7:03pm

Hi @njeffery

You can WMA to do this. Here is the function:

github.com

SlicerDMRI/whitematteranalysis/blob/8dc9674e125971ff039b38a1911444550049cf0e/whitematteranalysis/filter.py#L99

      
        
                    pd2 = downsample(pd, fibers_per_bin,verbose=False)
                    if verbose:
                        print(pd2.GetNumberOfLines(), "fibers in length range:", [bin_low, bin_hi])
                    if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
                        appender.AddInputData(pd2)
                    else:
                        appender.AddInput(pd2)
                appender.Update()
                return(appender.GetOutput())
            
            
def compute_lengths(inpd):
                """Compute length of each fiber in polydata. Returns lengths and step size.
            
            
    Step size is estimated using points in the middle of a fiber with over 15 points.
            
            
    """
            
            
    # Make sure we have lines and points.
                if (inpd.GetNumberOfLines() == 0) or (inpd.GetNumberOfPoints() == 0):
                    print("<filter.py> No fibers found in input polydata.")
                    return 0, 0

It seems you have tried WMA. Wonder what you meant that you cannot get it to work. Is it an installation problem?

Thanks,
Fan

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Fibre length measurements

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