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Ayan Sengupta edited Methods.tex
over 9 years ago
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Phase unwrapping is performed by FSL PRELUDE tool. Slicewise phase unwrapping is performed, which is a quicker process but 3D volume wise phase is much slower but very robust.
\item \textbf{Step 2: Spatial High Pass Filtering}
Spatial High pass filtering of the phase unwrapped images is performed by subtracting the spatially smoothed image from the original image. For spatial smoothing, a gaussian kernel is used and as a rule of thumb, the sigma of the kernel is taken as 3*voxel dimension. In this case it is approximated
\~1.3mm. \textasciitilde1.3mm.
\item \textbf{Step 3: Voxelwise Product of Magnitude and Phase Unwrapped Image}
The spatially high pass filtered phase unwrapped image is multiplied with the magnitude image in FSL, to generate a volume in which the veins are represented as white voxels. A binary mask for veins can be generated by restricting the volume thus generated to a particular ROI, normalizing and scaling to a predetermined intensity range.