Python MinImage示例

示例#1

#
###########
# merging cope files
copemerge = Node(fsl.Merge(dimension='t', in_files=listCopeFiles),
                 name="copemerge")

# merging varcope files
varcopemerge = Node(fsl.Merge(dimension='t', in_files=listVarcopeFiles),
                    name="varcopemerge")

# merging mask files
maskmerge = Node(fsl.Merge(dimension='t', in_files=listMaskFiles),
                 name="maskmerge")

# calculating the minimum across time points on merged mask image
minmask = Node(fsl.MinImage(), name="minmask")

# creating datasink to collect outputs
datasink = Node(DataSink(base_directory=os.path.join(
    outDir, 'FingerFootLips_Test_Cope6_Handedness')),
                name='datasink')

###########
#
# SETTING UP THE WORKFLOW NODES
#
###########

# creating the workflow
secondLevel = Workflow(name="Level2", base_dir=outDir)

示例#2

文件： porcupine_generated_pipeline.py 项目： GiraffeTools/Documentation

                               iterfield=['value'])
NodeHash_16852000.inputs.percentage = 0.75

#Custom interface wrapping function Getpercentthresh
NodeHash_16878250 = pe.MapNode(interface=firstlevelhelpers.Getpercentthresh,
                               name='NodeName_16878250',
                               iterfield=['value'])
NodeHash_16878250.inputs.percentage = 0.1

#Wraps command **fslmaths**
NodeHash_171fdb30 = pe.MapNode(interface=fsl.Threshold(),
                               name='NodeName_171fdb30',
                               iterfield=['in_file', 'thresh'])

#Wraps command **fslmaths**
NodeHash_179e1da0 = pe.MapNode(interface=fsl.MinImage(),
                               name='NodeName_179e1da0',
                               iterfield=['in_file'])
NodeHash_179e1da0.inputs.args = '-bin'
NodeHash_179e1da0.inputs.dimension = 'T'

#Wraps command **fslmaths**
NodeHash_1879dad0 = pe.MapNode(interface=fsl.ChangeDataType(),
                               name='NodeName_1879dad0',
                               iterfield=['in_file'])
NodeHash_1879dad0.inputs.output_datatype = 'char'

#Wraps command **fslmaths**
NodeHash_188ac400 = pe.MapNode(interface=fsl.DilateImage(),
                               name='NodeName_188ac400',
                               iterfield=['in_file'])

示例#3

#Custom interface wrapping function Tsv2subjectinfo
NodeHash_1ad39010 = pe.MapNode(interface = firstlevelhelpers.Tsv2subjectinfo, name = 'NodeName_1ad39010', iterfield = ['in_file'])

#Custom interface wrapping function Getpercentthresh
NodeHash_1cecfcd0 = pe.MapNode(interface = firstlevelhelpers.Getpercentthresh, name = 'NodeName_1cecfcd0', iterfield = ['value'])
NodeHash_1cecfcd0.inputs.percentage = 0.75

#Custom interface wrapping function Getpercentthresh
NodeHash_20695ac0 = pe.MapNode(interface = firstlevelhelpers.Getpercentthresh, name = 'NodeName_20695ac0', iterfield = ['value'])
NodeHash_20695ac0.inputs.percentage = 0.1

#Wraps command **fslmaths**
NodeHash_10ff9c60 = pe.MapNode(interface = fsl.Threshold(), name = 'NodeName_10ff9c60', iterfield = ['in_file', 'thresh'])

#Wraps command **fslmaths**
NodeHash_843b4a0 = pe.MapNode(interface = fsl.MinImage(), name = 'NodeName_843b4a0', iterfield = ['in_file'])
NodeHash_843b4a0.inputs.args = '-bin'
NodeHash_843b4a0.inputs.dimension = 'T'

#Wraps command **fslmaths**
NodeHash_2b6977b0 = pe.MapNode(interface = fsl.ChangeDataType(), name = 'NodeName_2b6977b0', iterfield = ['in_file'])
NodeHash_2b6977b0.inputs.output_datatype = 'char'

#Wraps command **fslmaths**
NodeHash_258767c0 = pe.MapNode(interface = fsl.DilateImage(), name = 'NodeName_258767c0', iterfield = ['in_file'])
NodeHash_258767c0.inputs.operation = 'max'

#Wraps command **fslstats**
NodeHash_2fd0bda0 = pe.MapNode(interface = fsl.ImageStats(), name = 'NodeName_2fd0bda0', iterfield = ['in_file', 'mask_file'])
NodeHash_2fd0bda0.inputs.op_string = '-p 50'

示例#4

文件： porcupine_generated_workflow.py 项目： kaczmarj/Porcupine

#Custom interface wrapping function Tsv2subjectinfo
NodeHash_127d16f0 = pe.MapNode(interface = firstlevelhelpers.Tsv2subjectinfo, name = 'NodeName_127d16f0', iterfield = ['in_file'])

#Custom interface wrapping function Getpercentthresh
NodeHash_14e113c0 = pe.MapNode(interface = firstlevelhelpers.Getpercentthresh, name = 'NodeName_14e113c0', iterfield = ['value'])
NodeHash_14e113c0.inputs.percentage = 0.75

#Custom interface wrapping function Getpercentthresh
NodeHash_14e3d7c0 = pe.MapNode(interface = firstlevelhelpers.Getpercentthresh, name = 'NodeName_14e3d7c0', iterfield = ['value'])
NodeHash_14e3d7c0.inputs.percentage = 0.1

#Wraps command **fslmaths**
NodeHash_157bd2b0 = pe.MapNode(interface = fsl.Threshold(), name = 'NodeName_157bd2b0', iterfield = ['in_file', 'thresh'])

#Wraps command **fslmaths**
NodeHash_15f74220 = pe.MapNode(interface = fsl.MinImage(), name = 'NodeName_15f74220', iterfield = ['in_file'])
NodeHash_15f74220.inputs.args = '-bin'
NodeHash_15f74220.inputs.dimension = 'T'

#Wraps command **fslmaths**
NodeHash_16d421a0 = pe.MapNode(interface = fsl.ChangeDataType(), name = 'NodeName_16d421a0', iterfield = ['in_file'])
NodeHash_16d421a0.inputs.output_datatype = 'char'

#Wraps command **fslmaths**
NodeHash_1801caa0 = pe.MapNode(interface = fsl.DilateImage(), name = 'NodeName_1801caa0', iterfield = ['in_file'])
NodeHash_1801caa0.inputs.operation = 'max'

#Wraps command **fslstats**
NodeHash_18508680 = pe.MapNode(interface = fsl.ImageStats(), name = 'NodeName_18508680', iterfield = ['in_file', 'mask_file'])
NodeHash_18508680.inputs.op_string = '-p 50'