[Mrtrix-discussion] sf problem

[Georg Kerbler]

Hi

I'm having some trouble with the single fibre mask for one of my subjects; sf.mif is at an angle compared to FA and to rawdata (see attached screenshot).
My commands were:
$ dwi2tensor rawdata.mif tensor.mif
$ tensor_metric tensor.mif -fa fa.nii 
$ mrconvert rawdata.mif -coord 3 0 - | threshold - - | median3D - - | median3D - - | erode - - | erode - - | erode - - | mrmult - fa.nii - | threshold - -abs 0.6 sf.mif

I haven't seen this problem for any other subjects. Any suggestions?

Thanks
Georg

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