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designer.preprocessing.smoothing.
nansmooth
(imgslice, fwhm)¶ Smooths an image slice while ignoring NaNs
- Parameters
imgslice ((X x Y) img_like or array_like object) – 2D image to be smoothed
fwhm (float) – The full width half max to be used for smoothing
- Returns
smoothslice – 2D smoothed image
- Return type
(X x Y) array_like object
Notes
This is done because a masked dataset will contain NaNs. In typical operations and filtering, the NaNs will propagate instead of being ignored (which is the desired behavior). During runtime, divide by 0 warnings are suppressed due to the high probability of its occuring. The operation to avoid this is as follows:
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designer.preprocessing.smoothing.
smooth
(dwi, csfmask=None, width=1.25)¶ Smooths a DWI dataset
- Parameters
dwi ((X x Y x Z x N) img_like object) – Image to be smoothed, where N is the number of volumes in the DWI acquisition.
csfmask ((S) img_like object) – The mask of CSF that will be applied to each volume in DWI
width (float, optional) – The full width half max in voxels to be smoothed. Default: 1.25
- Returns
smoothed – The smoothed version of dwi
- Return type
(X x Y x Z x N) array_like or img_like object
Notes
This is done mainly to reduce the Gibbs ringing. It might be recommended to only smooth the high SNR (or b-valued) data in order not to alter the Rice distribution of the low SNR data. This is important to maintain the high accuracy of WLLS. If a CSF mask is given as an additional argument, CSF infiltration in microstructural signal is avoided during smoothing.
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designer.preprocessing.smoothing.
smooth_image
(dwiname, csfname=None, outname='dwism.nii', width=1.2)¶ Smooths a DWI dataset
- Parameters
dwiname (str) – Filename of image to be smoothed
csfname (str) – Filename of CSF mask
outname (str) – Filename to be written out
width (float) – The full width half max in voxels to be smoothed. Default: 1.25
- Returns
- Return type
None; writes out file
See also
smooth()
,csfmask()
,width()