In [29]:

    

## Boiler plate code common to many notebooks.  See the TestFilesCommonCode.ipynb for details
from __future__ import print_function
%run TestFilesCommonCode.ipynb


    

    




SimpleITK Version: 1.0.1 (ITK 4.11)
Compiled: Aug  7 2017 12:11:31

In [30]:

    

img_labels_filename = '/Volumes/G-RAID1/Ali/rat_rsfMRI_phMRI/data/atlas/invicroRatAtlas.nii'
img_labels = sitk.ReadImage(img_labels_filename)
print(img_labels.GetPixelIDTypeAsString())
img_labels = sitk.Cast(img_labels,sitk.sitkUInt32)
print(img_labels.GetPixelIDTypeAsString())
myshow(sitk.LabelToRGB(img_labels))


    

    




32-bit float
32-bit unsigned integer






    

In [31]:

    

# inclusionLables = sitk.Image(img_labels.GetSize(), sitk.sitkUInt64)
# inclusionLables.SetOrigin(img_labels.GetOrigin())
# inclusionLables.SetSpacing(img_labels.GetSpacing())
# print(inclusionLables.GetPixelIDTypeAsString())

# minmax = sitk.MinimumMaximumImageFilter()
# minmax.Execute(inclusionLables)
# print(minmax.GetMaximum())
# print(minmax.GetMinimum())


    

In [32]:

    

minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(img_labels)
print(minmax.GetMaximum())
print(minmax.GetMinimum())


    

    




3203.0
0.0

In [33]:

    

Cingulate=(img_labels == 1034)+(img_labels == 1434)
Retrosplenial=(img_labels == 1135)+(img_labels == 1535)
LeftHippocampus=(img_labels == 1062)+(img_labels == 1063)+(img_labels == 1064)+(img_labels == 1065)+(img_labels == 1066)
RightHippocampus=(img_labels == 1462)+(img_labels == 1463)+(img_labels == 1464)+(img_labels == 1465)+(img_labels == 1466)
LeftPrimarySomatosensory=(img_labels == 1143)+(img_labels == 1144)+(img_labels == 1145)+(img_labels == 1146)+(img_labels == 1147)+(img_labels == 1148)+(img_labels == 1149)+(img_labels == 1150)+(img_labels == 1151)+(img_labels == 1152)
RightPrimarySomatosensory=(img_labels == 1543)+(img_labels == 1544)+(img_labels == 1545)+(img_labels == 1546)+(img_labels == 1547)+(img_labels == 1548)+(img_labels == 1549)+(img_labels == 1550)+(img_labels == 1551)+(img_labels == 1552)
LeftMotor=(img_labels == 1083)+(img_labels == 1084)
RightMotor=(img_labels == 1483)+(img_labels == 1484)
Caudate=(img_labels == 1157)
Putamen=(img_labels == 1557)
LeftAccumbens=(img_labels == 1053)+(img_labels == 1159)
RightAccumbens=(img_labels == 1453)+(img_labels == 1559)


    

In [34]:

    

Cingulate = sitk.Cast(Cingulate,sitk.sitkUInt32)
Retrosplenial = sitk.Cast(Retrosplenial,sitk.sitkUInt32)
LeftHippocampus = sitk.Cast(LeftHippocampus,sitk.sitkUInt32)
RightHippocampus = sitk.Cast(RightHippocampus,sitk.sitkUInt32)
LeftPrimarySomatosensory = sitk.Cast(LeftPrimarySomatosensory,sitk.sitkUInt32)
RightPrimarySomatosensory = sitk.Cast(RightPrimarySomatosensory,sitk.sitkUInt32)
LeftMotor = sitk.Cast(LeftMotor,sitk.sitkUInt32)
RightMotor = sitk.Cast(RightMotor,sitk.sitkUInt32)
Caudate = sitk.Cast(Caudate,sitk.sitkUInt32)
Putamen = sitk.Cast(Putamen,sitk.sitkUInt32)
LeftAccumbens = sitk.Cast(LeftAccumbens,sitk.sitkUInt32)
RightAccumbens = sitk.Cast(RightAccumbens,sitk.sitkUInt32)


    

In [35]:

    

minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(Cingulate)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(Retrosplenial)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(LeftHippocampus)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(RightHippocampus)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(LeftPrimarySomatosensory)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(RightPrimarySomatosensory)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(LeftMotor)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(RightMotor)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(Caudate)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(Putamen)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(LeftAccumbens)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')
minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(RightAccumbens)
print(minmax.GetMaximum())
print(minmax.GetMinimum())
print('-----')


    

    




1.0
0.0
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1.0
0.0
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1.0
0.0
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1.0
0.0
-----
1.0
0.0
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1.0
0.0
-----
1.0
0.0
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1.0
0.0
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1.0
0.0
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1.0
0.0
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1.0
0.0
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1.0
0.0
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In [36]:

    

inclusionLables=(Cingulate*2034 + 
                 + Retrosplenial*2135
                 + LeftHippocampus*2062
                 + RightHippocampus*2462
                 + LeftPrimarySomatosensory*2143
                 + RightPrimarySomatosensory*2543
                 + LeftMotor*2083
                 + RightMotor*2483
                 + Caudate*1157
                 + Putamen*1557
                 + LeftAccumbens*1205
                 + RightAccumbens*1605)

print(inclusionLables.GetPixelIDTypeAsString())

minmax = sitk.MinimumMaximumImageFilter()
minmax.Execute(inclusionLables)
print(minmax.GetMaximum())
print(minmax.GetMinimum())

myshow(sitk.LabelToRGB(inclusionLables))


    

    




32-bit unsigned integer
2543.0
0.0






    

In [37]:

    

sitk.WriteImage(inclusionLables,'/Volumes/G-RAID1/Ali/rat_rsfMRI_phMRI/data/atlas/invicroRatAtlas_for_seedbased_correlation.nii')


    

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