first mipav pipeline

Author: chrisgorgo

examples/smri_cbs_skullstripping.py

@@ -0,0 +1,27 @@
+import nipype.interfaces.io as nio           # Data i/o
+import nipype.interfaces.utility as util     # utility
+import nipype.pipeline.engine as pe          # pypeline engine
+import nipype.interfaces.camino as camino
+import nipype.interfaces.fsl as fsl
+import nipype.interfaces.camino2trackvis as cam2trk
+import nipype.algorithms.misc as misc
+import os  
+from nipype.interfaces.mipav.developer import JistIntensityMp2rageMasking, MedicAlgorithmSPECTRE2010
+
+wf = pe.Workflow("skullstripping")
+
+mask = pe.Node(JistIntensityMp2rageMasking(), name="masking")
+mask.inputs.inSecond = "/scr/adenauer1/7T_TRT/pilot/data/OK2T140312_093516.SEPT/nifti/S4_MP2RAGE_5_3_TR5000_iPAT=2_INV2.nii"
+mask.inputs.inQuantitative = "/scr/adenauer1/7T_TRT/pilot/data/OK2T140312_093516.SEPT/nifti/S7_MP2RAGE_5_3_TR5000_iPAT=2_UNI_Images.nii"
+mask.inputs.inT1weighted = "/scr/adenauer1/7T_TRT/pilot/data/OK2T140312_093516.SEPT/nifti/S6_MP2RAGE_5_3_TR5000_iPAT=2_T1_Images.nii"
+mask.inputs.outMasked = True
+mask.inputs.outMasked2 = True
+mask.inputs.outSignal = True
+mask.inputs.outSignal2 = True
+
+skullstrip = pe.Node(MedicAlgorithmSPECTRE2010(), name="skullstrip")
+skullstrip.inputs.outStripped = True
+skullstrip.inputs.maxMemoryUsage = 6000
+
+wf.connect(mask, 'outMasked', skullstrip, 'inInput')
+wf.run()

nipype/interfaces/mipav/developer.py

@@ -7,7 +7,7 @@
 
 
 class MedicAlgorithmSPECTRE2010InputSpec(CommandLineInputSpec):
-    maxMemoryUsage = traits.Int(desc="Maximum Memory Allowed (in MegaBytes). Increase or decrease this depending on java virtual machine heap size requirements.", argstr="--maxMemoryUsage %d")
+    maxMemoryUsage = traits.Int(desc="Maximum Memory Allowed (in MegaBytes). Increase or decrease this depending on java virtual machine heap size requirements.", argstr="-xDefaultMem %d")
     inInput = File(desc="Input volume to be skullstripped.", exists=True, argstr="--inInput %s")
     inAtlas = File(desc="SPECTRE atlas description file. A text file enumerating atlas files and landmarks.", exists=True, argstr="--inAtlas %s")
     inInitial = traits.Int(desc="Erosion of the inital mask, which is based on the probability mask and the classification., The initial mask is ouput as the d0 volume at the conclusion of SPECTRE.", argstr="--inInitial %d")