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BUGFIX: median otsu parameters to latest dipy version. (#88)
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@rutgerfick
rutgerfick committed Apr 29, 2020
1 parent 0959ca9 commit c8b5d66
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2 changes: 1 addition & 1 deletion dmipy/tissue_response/three_tissue_response.py
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Expand Up @@ -82,7 +82,7 @@ def three_tissue_response_dhollander16(
SDM = signal_decay_metric(acquisition_scheme, data)

# Make Mask
b0_mask, mask = median_otsu(data, 2, 1)
b0_mask, mask = median_otsu(data, median_radius=2, numpass=1)

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@heejong-kim

heejong-kim May 4, 2020

@rutgerfick Hello, thank you for the quick fix on this. Could you check and update the b0 indices as well? You can simply replace the line with b0_mask, mask = median_otsu(data, np.where(acquisition_scheme.b0_mask)[0], median_radius=2, numpass=1). The otsu_median makes use of b0 images to mask the 4d DWI data and the variable for indices is missing in the script.

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@rutgerfick

rutgerfick May 11, 2020

Author Collaborator

done in #92 :)
gtab = gtab_dmipy2dipy(acquisition_scheme)
tenmod = dti.TensorModel(gtab)
tenfit = tenmod.fit(b0_mask)
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2 changes: 1 addition & 1 deletion dmipy/version.py
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Expand Up @@ -4,7 +4,7 @@
# Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"
_version_major = 1
_version_minor = 0
_version_micro = 2 # use '' for first of series, number for 1 and above
_version_micro = 3 # use '' for first of series, number for 1 and above
_version_extra = ''
# _version_extra = '' # Uncomment this for full releases

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