from nipype.interfaces import mipav
import nipype.interfaces.mipav.gilles
from nipype.interfaces.mipav.developer import *
skullstrip = mipav.gilles.JistBrainMp2rageSkullStripping()
skullstrip.inputs.inSecond = '/home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii'
skullstrip.inputs.inFilter = '/home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii'
skullstrip.inputs.inT1weighted = '/home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii'
skullstrip.inputs.outBrain = True
skullstrip.cmdline
'/home/gdholla1/mipav/jre/bin/java -classpath /home/gdholla1/mipav/plugins/:/home/gdholla1/mipav/:/home/gdholla1/mipav/Uninstall-MIPAV/uninstaller.jar:/home/gdholla1/mipav/lib/jaxp/xalan.jar:/home/gdholla1/mipav/lib/jaxp/xercesImpl.jar:/home/gdholla1/mipav/lib/jaxp/dom.jar:/home/gdholla1/mipav/lib/jaxp/sax.jar:/home/gdholla1/mipav/lib/bcprov-jdk15-136.jar:/home/gdholla1/mipav/lib/mail.jar:/home/gdholla1/mipav/lib/policy.jar:/home/gdholla1/mipav/lib/jdom.jar:/home/gdholla1/mipav/lib/jj2kpack.jar:/home/gdholla1/mipav/lib/core_dictionary-4.1.1.8.jar:/home/gdholla1/mipav/lib/javax.persistence.jar:/home/gdholla1/mipav/lib/hyperapplet.jar:/home/gdholla1/mipav/lib/jaxb-api.jar:/home/gdholla1/mipav/lib/fitbir-model.jar:/home/gdholla1/mipav/lib/jhall.jar:/home/gdholla1/mipav/lib/stax-ex.jar:/home/gdholla1/mipav/lib/WildMagic.jar:/home/gdholla1/mipav/lib/camino.jar:/home/gdholla1/mipav/lib/jaxb-impl.jar:/home/gdholla1/mipav/lib/jTEM.jar:/home/gdholla1/mipav/lib/activation.jar:/home/gdholla1/mipav/lib/saaj-impl.jar:/home/gdholla1/mipav/lib/JimiProClasses.jar:/home/gdholla1/mipav/lib/tar.jar:/home/gdholla1/mipav/lib/fontbox-1.2.0.jar:/home/gdholla1/mipav/lib/log4j-1.2.16.jar:/home/gdholla1/mipav/lib/dataDictionaryClient-4.1.1.8.jar:/home/gdholla1/mipav/lib/streambuffer.jar:/home/gdholla1/mipav/lib/jaxws-rt.jar:/home/gdholla1/mipav/lib/ij.jar:/home/gdholla1/mipav/lib/jax-qname.jar:/home/gdholla1/mipav/lib/gmbal-api-only.jar:/home/gdholla1/mipav/lib/javac.jar:/home/gdholla1/mipav/lib/pdfbox-1.2.0.jar:/home/gdholla1/mipav/lib/jempbox-1.2.0.jar:/home/gdholla1/mipav/lib/fitbir-web-service.jar:/home/gdholla1/mipav/lib/ACCESSION_client_VTool.jar:/home/gdholla1/mipav/lib/junit-4.4.jar:/home/gdholla1/mipav/jre/lib/resources.jar:/home/gdholla1/mipav/jre/lib/charsets.jar:/home/gdholla1/mipav/jre/lib/alt-rt.jar:/home/gdholla1/mipav/jre/lib/deploy.jar:/home/gdholla1/mipav/jre/lib/rt.jar:/home/gdholla1/mipav/jre/lib/jsse.jar:/home/gdholla1/mipav/jre/lib/jce.jar:/home/gdholla1/mipav/jre/lib/management-agent.jar:/home/gdholla1/mipav/jre/lib/alt-string.jar:/home/gdholla1/mipav/jre/lib/javaws.jar:/home/gdholla1/mipav/jre/lib/ext/jogl.all-mobile.jar:/home/gdholla1/mipav/jre/lib/ext/joal-test.jar:/home/gdholla1/mipav/jre/lib/ext/newt.event.jar:/home/gdholla1/mipav/jre/lib/ext/j3dcore.jar:/home/gdholla1/mipav/jre/lib/ext/sunjce_provider.jar:/home/gdholla1/mipav/jre/lib/ext/jogl.all-noawt.jar:/home/gdholla1/mipav/jre/lib/ext/customizer.jar:/home/gdholla1/mipav/jre/lib/ext/multiplayer.jar:/home/gdholla1/mipav/jre/lib/ext/jhdfobj.jar:/home/gdholla1/mipav/jre/lib/ext/gluegen.jar:/home/gdholla1/mipav/jre/lib/ext/gluegen-rt.jar:/home/gdholla1/mipav/jre/lib/ext/jocl.jar:/home/gdholla1/mipav/jre/lib/ext/joal.jar:/home/gdholla1/mipav/jre/lib/ext/vecmath.jar:/home/gdholla1/mipav/jre/lib/ext/JOCL-0.1.7.jar:/home/gdholla1/mipav/jre/lib/ext/mediaplayer.jar:/home/gdholla1/mipav/jre/lib/ext/jhdf5obj.jar:/home/gdholla1/mipav/jre/lib/ext/jogl.all.jar:/home/gdholla1/mipav/jre/lib/ext/jogl.test.jar:/home/gdholla1/mipav/jre/lib/ext/sunpkcs11.jar:/home/gdholla1/mipav/jre/lib/ext/j3dutils.jar:/home/gdholla1/mipav/jre/lib/ext/jmf.jar:/home/gdholla1/mipav/jre/lib/ext/jhdf5.jar:/home/gdholla1/mipav/jre/lib/ext/dnsns.jar:/home/gdholla1/mipav/jre/lib/ext/localedata.jar:/home/gdholla1/mipav/jre/lib/im/thaiim.jar:/home/gdholla1/mipav/jre/lib/im/indicim.jar:/home/gdholla1/mipav/jre/lib/security/local_policy.jar:/home/gdholla1/mipav/jre/lib/security/US_export_policy.jar:/home/gdholla1/mipav/jre/lib/plugin.jar:/home/gdholla1/mipav/plugins/methods/methods.jar:/home/gdholla1/mipav/plugins/library/nativewindow.all.jar:/home/gdholla1/mipav/plugins/library/gluegen-rt.jar:/home/gdholla1/mipav/plugins/library/jogl.all.jar:/home/gdholla1/mipav/help/mipav_help.jar:/home/gdholla1/mipav/lax.jar:/home/gdholla1/mipav/InsightToolkit/lib/InsightToolkit/InsightToolkit.jar edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping --inFilter /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii --inInv2 /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii --inT1weighted /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii --outBrain /home/gdholla1/notebooks/outBrain.nii -xMaxProcess 1'
skullstrip.inputs
args = <undefined> environ = {} ignore_exception = False inFilter = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii inSecond = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii inSkip = <undefined> inT1 = <undefined> inT1weighted = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii null = <undefined> outBrain = True outMasked = <undefined> outMasked2 = <undefined> outMasked3 = <undefined> terminal_output = stream xDefaultMem = <undefined> xMaxProcess = 1 xPrefExt = <undefined>
r = skullstrip.run()
INFO:interface:stderr 2014-10-08T11:20:20.836197:Could not find library, using working directory /home/gdholla1/jist-lib INFO:interface:stdout 2014-10-08T11:20:20.884448:cli #################################################################### INFO:interface:stdout 2014-10-08T11:20:20.884448:cli Initializing MIPAV/JIST Framework INFO:interface:stdout 2014-10-08T11:20:20.902357:MIPAV STARTED with forceQuite set as true INFO:interface:stdout 2014-10-08T11:20:21.345067:cli #################################################################### INFO:interface:stdout 2014-10-08T11:20:21.345067:cli Interpretting command line arguments INFO:interface:stdout 2014-10-08T11:20:21.346911:cli #################################################################### INFO:interface:stdout 2014-10-08T11:20:21.346911:de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping INFO:interface:stdout 2014-10-08T11:20:21.346911: outExecution = <default> = INFO:interface:stdout 2014-10-08T11:20:21.346911: inSkip = <default> = false INFO:interface:stdout 2014-10-08T11:20:21.346911: inFilter = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii INFO:interface:stdout 2014-10-08T11:20:21.346911: outMasked2 = <default> = Masked T1-weighted Image INFO:interface:stdout 2014-10-08T11:20:21.346911: inInv2 = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii INFO:interface:stdout 2014-10-08T11:20:21.346911: inT1weighted = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii INFO:interface:stdout 2014-10-08T11:20:21.346911: outBrain = /home/gdholla1/notebooks/outBrain.nii = /home/gdholla1/notebooks/outBrain.nii INFO:interface:stdout 2014-10-08T11:20:21.346911: outMasked3 = <default> = Masked Filter Image INFO:interface:stdout 2014-10-08T11:20:21.346911: inT1 = <default> = T1 Map Image INFO:interface:stdout 2014-10-08T11:20:21.346911: outMasked = <default> = Masked T1 Map Image INFO:interface:stdout 2014-10-08T11:20:21.346911: outProc = /home/gdholla1/notebooks INFO:interface:stdout 2014-10-08T11:20:21.346911: outResult = output.txt INFO:interface:stdout 2014-10-08T11:20:21.346911:cli #################################################################### INFO:interface:stdout 2014-10-08T11:20:22.928623:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 0New image:256x256x176x1 INFO:interface:stdout 2014-10-08T11:20:23.594479:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 1New image:256x256x176x1 INFO:interface:stdout 2014-10-08T11:20:24.281982:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 2New image:256x256x176x1 INFO:interface:stdout 2014-10-08T11:20:28.052105:image range: 0.0, 1499.0 INFO:interface:stdout 2014-10-08T11:20:28.103567:mean parameters: 0.05102058095562509 INFO:interface:stdout 2014-10-08T11:20:28.773433:iteration 1 INFO:interface:stdout 2014-10-08T11:20:28.793751:mean parameters: 0.02495016508806164 INFO:interface:stdout 2014-10-08T11:20:28.796308:diff parameters: 0.026070415867563448 INFO:interface:stdout 2014-10-08T11:20:29.833239:iteration 2 INFO:interface:stdout 2014-10-08T11:20:29.856389:mean parameters: 0.013559674465951167 INFO:interface:stdout 2014-10-08T11:20:29.856767:diff parameters: 0.011390490622110474 INFO:interface:stdout 2014-10-08T11:20:30.924657:iteration 3 INFO:interface:stdout 2014-10-08T11:20:30.946159:mean parameters: 0.009698280057654995 INFO:interface:stdout 2014-10-08T11:20:30.946159:diff parameters: 0.003861394408296172 INFO:interface:stdout 2014-10-08T11:20:32.033618:iteration 4 INFO:interface:stdout 2014-10-08T11:20:32.055133:mean parameters: 0.008623307046790124 INFO:interface:stdout 2014-10-08T11:20:32.055784:diff parameters: 0.0010749730108648714 INFO:interface:stdout 2014-10-08T11:20:33.159937:iteration 5 INFO:interface:stdout 2014-10-08T11:20:33.181471:mean parameters: 0.008308390993678324 INFO:interface:stdout 2014-10-08T11:20:33.182087:diff parameters: 3.1491605311179983E-4 INFO:interface:stdout 2014-10-08T11:20:34.287089:iteration 6 INFO:interface:stdout 2014-10-08T11:20:34.308539:mean parameters: 0.008212212609716494 INFO:interface:stdout 2014-10-08T11:20:34.309467:diff parameters: 9.617838396182993E-5 INFO:interface:stdout 2014-10-08T11:20:35.645580:background-based skull strippingimage: [4.9592734E-5, 0.9918051] INFO:interface:stdout 2014-10-08T11:20:35.646195:scaled dimensions: 16 x 16 x 11 INFO:interface:stdout 2014-10-08T11:20:35.878608:min obj size: 2816 INFO:interface:stdout 2014-10-08T11:20:35.879032:max obj size: 278 INFO:interface:stdout 2014-10-08T11:20:35.879412:rng obj size: 1886 INFO:interface:stdout 2014-10-08T11:20:35.880508:and obj size: 278 INFO:interface:stdout 2014-10-08T11:20:35.907957:main obj size: 280 INFO:interface:stdout 2014-10-08T11:20:35.913368:boundary size: 228 INFO:interface:stdout 2014-10-08T11:20:35.922707:scaled dimensions: 32 x 32 x 22 INFO:interface:stdout 2014-10-08T11:20:36.187940:scaled dimensions: 64 x 64 x 44 INFO:interface:stdout 2014-10-08T11:20:36.560204:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 2Free image:S7_mp2rage_whole_brain_UNI_Images INFO:interface:stdout 2014-10-08T11:20:36.560204:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 1Free image:S6_mp2rage_whole_brain_T1_Images INFO:interface:stdout 2014-10-08T11:20:36.561505:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 0Free image:S4_mp2rage_whole_brain_INV2 INFO:interface:stdout 2014-10-08T11:20:36.824040:scaled dimensions: 128 x 128 x 88 INFO:interface:stdout 2014-10-08T11:20:41.865669:region size: 2049984 INFO:interface:stdout 2014-10-08T11:20:43.053107:LUT loaded from: file:/home/gdholla1/mipav/plugins/de/mpg/cbs/structures/critical66LUT.raw.gz INFO:interface:stdout 2014-10-08T11:20:43.273975:initialization INFO:interface:stdout 2014-10-08T11:20:43.274631:fast marching init INFO:interface:stdout 2014-10-08T11:20:45.026996:init INFO:interface:stdout 2014-10-08T11:20:54.955197:done INFO:interface:stdout 2014-10-08T11:20:54.999899:GDM forces: 0.0 (field), 0.1 (balloon), 0.9 (smoothing) INFO:interface:stdout 2014-10-08T11:20:55.698676:LUT loaded from: file:/home/gdholla1/mipav/plugins/de/mpg/cbs/structures/critical66LUT.raw.gz INFO:interface:stdout 2014-10-08T11:20:55.699317:initial GDM decomposition INFO:interface:stdout 2014-10-08T11:20:55.962001:fast marching INFO:interface:stdout 2014-10-08T11:20:56.301772:init INFO:interface:stdout 2014-10-08T11:21:10.551795:done INFO:interface:stdout 2014-10-08T11:21:10.552387:initialization INFO:interface:stdout 2014-10-08T11:21:10.552387:level set evolution: narrow band INFO:interface:stdout 2014-10-08T11:21:10.642527:init (1353272) INFO:interface:stdout 2014-10-08T11:21:10.771049:iteration 0 INFO:interface:stdout 2014-10-08T11:21:10.968725:changed labels: 3234 INFO:interface:stdout 2014-10-08T11:21:10.975238:iteration 1 INFO:interface:stdout 2014-10-08T11:21:11.127873:changed labels: 9607 INFO:interface:stdout 2014-10-08T11:21:11.135029:iteration 2 INFO:interface:stdout 2014-10-08T11:21:11.281653:changed labels: 4562 INFO:interface:stdout 2014-10-08T11:21:11.287681:iteration 3 INFO:interface:stdout 2014-10-08T11:21:11.431409:changed labels: 4510 INFO:interface:stdout 2014-10-08T11:21:11.437864:iteration 4 INFO:interface:stdout 2014-10-08T11:21:11.581141:changed labels: 4428 INFO:interface:stdout 2014-10-08T11:21:11.587094:iteration 5 INFO:interface:stdout 2014-10-08T11:21:11.729051:changed labels: 4019 INFO:interface:stdout 2014-10-08T11:21:11.735478:iteration 6 INFO:interface:stdout 2014-10-08T11:21:11.878011:changed labels: 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image:256x256x176x0 INFO:interface:stderr 2014-10-08T11:21:29.268109:edu.jhu.ece.iacl.jist.pipeline.CalculationMonitorCalculation Monitor not running. Punting stop. INFO:interface:stdout 2014-10-08T11:21:29.273330:---------- Performance Summary ---------- INFO:interface:stdout 2014-10-08T11:21:29.273330:1) Algorithm Calculation -- ELAPSED TIME: Actual: 1 min 7.91 sec / CPU: 1 min 7.42 sec INFO:interface:stdout 2014-10-08T11:21:29.273330: INFO:interface:stdout 2014-10-08T11:21:29.273330:TOTAL ELAPSED TIME: Actual: 1 min 7.91 sec / CPU: 1 min 7.42 sec INFO:interface:stdout 2014-10-08T11:21:29.273330:CURRENT MEMORY: Used 671 MB, Free 1259 MB, Total 1930 MB INFO:interface:stdout 2014-10-08T11:21:29.274824:jist.io FileReaderWriter: write file:outBrain.nii INFO:interface:stderr 2014-10-08T11:21:29.275134:edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher stopping via interrupt. INFO:interface:stderr 2014-10-08T11:21:29.275134:edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher finished. INFO:interface:stdout 2014-10-08T11:21:29.631453:%% outBrain.nii INFO:interface:stdout 2014-10-08T11:21:29.631453:%% /home/gdholla1/notebooks INFO:interface:stdout 2014-10-08T11:21:29.631453:== /home/gdholla1/notebooks/outBrain.nii INFO:interface:stdout 2014-10-08T11:21:29.966910:cli #################################################################### INFO:interface:stdout 2014-10-08T11:21:29.967730:cli Done: de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping INFO:interface:stdout 2014-10-08T11:21:29.967730:cli ####################################################################
r.outputs
outBrain = /home/gdholla1/notebooks/outBrain.nii outMasked = <undefined> outMasked2 = <undefined> outMasked3 = <undefined>
skullstrip = mipav.gilles.JistBrainMp2rageSkullStripping()
skullstrip.inputs.inSecond = '/home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii'
skullstrip.inputs.inFilter = '/home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii'
skullstrip.inputs.inT1weighted = '/home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii'
skullstrip.inputs.outMasked = True
r = skullstrip.run()
INFO:interface:stderr 2014-10-08T11:25:02.881060:Could not find library, using working directory /home/gdholla1/jist-lib INFO:interface:stdout 2014-10-08T11:25:02.929357:cli #################################################################### INFO:interface:stdout 2014-10-08T11:25:02.929357:cli Initializing MIPAV/JIST Framework INFO:interface:stdout 2014-10-08T11:25:02.946875:MIPAV STARTED with forceQuite set as true INFO:interface:stdout 2014-10-08T11:25:03.373111:cli #################################################################### INFO:interface:stdout 2014-10-08T11:25:03.373111:cli Interpretting command line arguments INFO:interface:stdout 2014-10-08T11:25:03.374932:cli #################################################################### INFO:interface:stdout 2014-10-08T11:25:03.374932:de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping INFO:interface:stdout 2014-10-08T11:25:03.374932: outExecution = <default> = INFO:interface:stdout 2014-10-08T11:25:03.374932: inSkip = <default> = false INFO:interface:stdout 2014-10-08T11:25:03.374932: inFilter = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii INFO:interface:stdout 2014-10-08T11:25:03.374932: outMasked2 = <default> = Masked T1-weighted Image INFO:interface:stdout 2014-10-08T11:25:03.374932: inInv2 = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii INFO:interface:stdout 2014-10-08T11:25:03.374932: inT1weighted = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii INFO:interface:stdout 2014-10-08T11:25:03.374932: outBrain = <default> = Brain Mask Image INFO:interface:stdout 2014-10-08T11:25:03.374932: outMasked3 = <default> = Masked Filter Image INFO:interface:stdout 2014-10-08T11:25:03.374932: inT1 = <default> = T1 Map Image INFO:interface:stdout 2014-10-08T11:25:03.374932: outMasked = /home/gdholla1/notebooks/outMasked.nii = /home/gdholla1/notebooks/outMasked.nii INFO:interface:stdout 2014-10-08T11:25:03.374932: outProc = /home/gdholla1/notebooks INFO:interface:stdout 2014-10-08T11:25:03.374932: outResult = output.txt INFO:interface:stdout 2014-10-08T11:25:03.379824:cli #################################################################### INFO:interface:stdout 2014-10-08T11:25:04.957285:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 0New image:256x256x176x1 INFO:interface:stdout 2014-10-08T11:25:05.657154:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 1New image:256x256x176x1 INFO:interface:stdout 2014-10-08T11:25:06.349454:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 2New image:256x256x176x1 INFO:interface:stdout 2014-10-08T11:25:09.207651:image range: 0.0, 1499.0 INFO:interface:stdout 2014-10-08T11:25:09.257496:mean parameters: 0.05102058095562509 INFO:interface:stdout 2014-10-08T11:25:09.934716:iteration 1 INFO:interface:stdout 2014-10-08T11:25:09.957078:mean parameters: 0.02495016508806164 INFO:interface:stdout 2014-10-08T11:25:09.960048:diff parameters: 0.026070415867563448 INFO:interface:stdout 2014-10-08T11:25:10.995837:iteration 2 INFO:interface:stdout 2014-10-08T11:25:11.019106:mean parameters: 0.013559674465951167 INFO:interface:stdout 2014-10-08T11:25:11.020090:diff parameters: 0.011390490622110474 INFO:interface:stdout 2014-10-08T11:25:12.085825:iteration 3 INFO:interface:stdout 2014-10-08T11:25:12.109079:mean parameters: 0.009698280057654995 INFO:interface:stdout 2014-10-08T11:25:12.109079:diff parameters: 0.003861394408296172 INFO:interface:stdout 2014-10-08T11:25:13.197874:iteration 4 INFO:interface:stdout 2014-10-08T11:25:13.219523:mean parameters: 0.008623307046790124 INFO:interface:stdout 2014-10-08T11:25:13.220184:diff parameters: 0.0010749730108648714 INFO:interface:stdout 2014-10-08T11:25:14.325797:iteration 5 INFO:interface:stdout 2014-10-08T11:25:14.348814:mean parameters: 0.008308390993678324 INFO:interface:stdout 2014-10-08T11:25:14.349659:diff parameters: 3.1491605311179983E-4 INFO:interface:stdout 2014-10-08T11:25:15.457711:iteration 6 INFO:interface:stdout 2014-10-08T11:25:15.480807:mean parameters: 0.008212212609716494 INFO:interface:stdout 2014-10-08T11:25:15.481615:diff parameters: 9.617838396182993E-5 INFO:interface:stdout 2014-10-08T11:25:16.799589:background-based skull strippingimage: [4.9592734E-5, 0.9918051] INFO:interface:stdout 2014-10-08T11:25:16.800355:scaled dimensions: 16 x 16 x 11 INFO:interface:stdout 2014-10-08T11:25:17.034147:min obj size: 2816 INFO:interface:stdout 2014-10-08T11:25:17.034898:max obj size: 278 INFO:interface:stdout 2014-10-08T11:25:17.034898:rng obj size: 1886 INFO:interface:stdout 2014-10-08T11:25:17.036117:and obj size: 278 INFO:interface:stdout 2014-10-08T11:25:17.063265:main obj size: 280 INFO:interface:stdout 2014-10-08T11:25:17.068559:boundary size: 228 INFO:interface:stdout 2014-10-08T11:25:17.078584:scaled dimensions: 32 x 32 x 22 INFO:interface:stdout 2014-10-08T11:25:17.349187:scaled dimensions: 64 x 64 x 44 INFO:interface:stdout 2014-10-08T11:25:17.694736:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 2Free image:S7_mp2rage_whole_brain_UNI_Images INFO:interface:stdout 2014-10-08T11:25:17.694736:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 1Free image:S6_mp2rage_whole_brain_T1_Images INFO:interface:stdout 2014-10-08T11:25:17.695869:edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 0Free image:S4_mp2rage_whole_brain_INV2 INFO:interface:stdout 2014-10-08T11:25:17.965736:scaled dimensions: 128 x 128 x 88 INFO:interface:stdout 2014-10-08T11:25:23.378723:region size: 2049984 INFO:interface:stdout 2014-10-08T11:25:24.594243:LUT loaded from: file:/home/gdholla1/mipav/plugins/de/mpg/cbs/structures/critical66LUT.raw.gz INFO:interface:stdout 2014-10-08T11:25:24.847777:initialization INFO:interface:stdout 2014-10-08T11:25:24.848595:fast marching init INFO:interface:stdout 2014-10-08T11:25:26.706797:init INFO:interface:stdout 2014-10-08T11:25:36.547019:done INFO:interface:stdout 2014-10-08T11:25:36.588853:GDM forces: 0.0 (field), 0.1 (balloon), 0.9 (smoothing) INFO:interface:stdout 2014-10-08T11:25:37.267279:LUT loaded from: file:/home/gdholla1/mipav/plugins/de/mpg/cbs/structures/critical66LUT.raw.gz INFO:interface:stdout 2014-10-08T11:25:37.267686:initial GDM decomposition INFO:interface:stdout 2014-10-08T11:25:37.525598:fast marching INFO:interface:stdout 2014-10-08T11:25:37.863837:init INFO:interface:stdout 2014-10-08T11:25:51.714237:done INFO:interface:stdout 2014-10-08T11:25:51.714817:initialization INFO:interface:stdout 2014-10-08T11:25:51.714817:level set evolution: narrow band INFO:interface:stdout 2014-10-08T11:25:51.805443:init (1353272) INFO:interface:stdout 2014-10-08T11:25:51.934626:iteration 0 INFO:interface:stdout 2014-10-08T11:25:52.131724:changed labels: 3234 INFO:interface:stdout 2014-10-08T11:25:52.137978:iteration 1 INFO:interface:stdout 2014-10-08T11:25:52.291084:changed labels: 9607 INFO:interface:stdout 2014-10-08T11:25:52.297405:iteration 2 INFO:interface:stdout 2014-10-08T11:25:52.442740:changed labels: 4562 INFO:interface:stdout 2014-10-08T11:25:52.449038:iteration 3 INFO:interface:stdout 2014-10-08T11:25:52.592742:changed labels: 4510 INFO:interface:stdout 2014-10-08T11:25:52.599012:iteration 4 INFO:interface:stdout 2014-10-08T11:25:52.742416:changed labels: 4428 INFO:interface:stdout 2014-10-08T11:25:52.748636:iteration 5 INFO:interface:stdout 2014-10-08T11:25:52.891356:changed labels: 4019 INFO:interface:stdout 2014-10-08T11:25:52.897651:iteration 6 INFO:interface:stdout 2014-10-08T11:25:53.039894:changed labels: 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image:256x256x176x0 INFO:interface:stderr 2014-10-08T11:26:10.555595:edu.jhu.ece.iacl.jist.pipeline.CalculationMonitorCalculation Monitor not running. Punting stop. INFO:interface:stdout 2014-10-08T11:26:10.561625:---------- Performance Summary ---------- INFO:interface:stdout 2014-10-08T11:26:10.561625:1) Algorithm Calculation -- ELAPSED TIME: Actual: 1 min 7.17 sec / CPU: 1 min 6.65 sec INFO:interface:stdout 2014-10-08T11:26:10.561625: INFO:interface:stdout 2014-10-08T11:26:10.561625:TOTAL ELAPSED TIME: Actual: 1 min 7.17 sec / CPU: 1 min 6.65 sec INFO:interface:stdout 2014-10-08T11:26:10.561625:CURRENT MEMORY: Used 1073 MB, Free 1359 MB, Total 2433 MB INFO:interface:stderr 2014-10-08T11:26:10.563303:edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher stopping via interrupt. INFO:interface:stderr 2014-10-08T11:26:10.563303:edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher finished. INFO:interface:stderr 2014-10-08T11:26:10.800118:java.io.IOException: NIFTI header file error INFO:interface:stderr 2014-10-08T11:26:10.800789: at gov.nih.mipav.model.file.FileNIFTI.readImage(FileNIFTI.java:2615) INFO:interface:stderr 2014-10-08T11:26:10.800789: at gov.nih.mipav.model.file.FileIO.readNIFTI(FileIO.java:8632) INFO:interface:stderr 2014-10-08T11:26:10.800789: at gov.nih.mipav.model.file.FileIO.readImage(FileIO.java:2449) INFO:interface:stderr 2014-10-08T11:26:10.800789: at gov.nih.mipav.model.file.FileIO.readImage(FileIO.java:2013) INFO:interface:stderr 2014-10-08T11:26:10.800789: at edu.jhu.ece.iacl.jist.io.ModelImageReaderWriter.readQuiet(ModelImageReaderWriter.java:116) INFO:interface:stdout 2014-10-08T11:26:10.802496:jist.io FileReaderWriter: write file:outMasked.nii INFO:interface:stdout 2014-10-08T11:26:10.802496:cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] -help INFO:interface:stdout 2014-10-08T11:26:10.802496:cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] [run options] INFO:interface:stdout 2014-10-08T11:26:10.802496:cli PARSE Error: null INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.io.ModelImageReaderWriter.readObject(ModelImageReaderWriter.java:84) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter.readObject(ImageDataReaderWriter.java:90) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter.readObject(ImageDataReaderWriter.java:34) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.io.FileReaderWriter.read(FileReaderWriter.java:69) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume.getImageData(ParamVolume.java:480) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume.getImageData(ParamVolume.java:469) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.cli.run.main(run.java:122) INFO:interface:stderr 2014-10-08T11:26:10.804104:FAILED to Open Volume from Disk: /home/gdholla1/notebooks/outMasked.nii INFO:interface:stderr 2014-10-08T11:26:10.804104:java.lang.NullPointerException INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav.createModelImage(ImageDataMipav.java:348) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter.writeObject(ImageDataReaderWriter.java:281) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter.writeObject(ImageDataReaderWriter.java:34) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.io.FileReaderWriter.write(FileReaderWriter.java:102) INFO:interface:stderr 2014-10-08T11:26:10.804104: at edu.jhu.ece.iacl.jist.cli.run.main(run.java:122)
--------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) <ipython-input-13-d2d5ab315aef> in <module>() ----> 1 r = skullstrip.run() /usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.pyc in run(self, **inputs) 996 runtime.environ['DISPLAY'] = ':%s' % vdisplay_num 997 --> 998 runtime = self._run_interface(runtime) 999 1000 if self._redirect_x: /usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.pyc in _run_interface(self, runtime, correct_return_codes) 1445 if runtime.returncode is None or \ 1446 runtime.returncode not in correct_return_codes: -> 1447 self.raise_exception(runtime) 1448 1449 return runtime /usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.pyc in raise_exception(self, runtime) 1374 message += "Standard error:\n" + runtime.stderr + "\n" 1375 message += "Return code: " + str(runtime.returncode) -> 1376 raise RuntimeError(message) 1377 1378 @classmethod RuntimeError: Command: /home/gdholla1/mipav/jre/bin/java -classpath /home/gdholla1/mipav/plugins/:/home/gdholla1/mipav/:/home/gdholla1/mipav/Uninstall-MIPAV/uninstaller.jar:/home/gdholla1/mipav/lib/jaxp/xalan.jar:/home/gdholla1/mipav/lib/jaxp/xercesImpl.jar:/home/gdholla1/mipav/lib/jaxp/dom.jar:/home/gdholla1/mipav/lib/jaxp/sax.jar:/home/gdholla1/mipav/lib/bcprov-jdk15-136.jar:/home/gdholla1/mipav/lib/mail.jar:/home/gdholla1/mipav/lib/policy.jar:/home/gdholla1/mipav/lib/jdom.jar:/home/gdholla1/mipav/lib/jj2kpack.jar:/home/gdholla1/mipav/lib/core_dictionary-4.1.1.8.jar:/home/gdholla1/mipav/lib/javax.persistence.jar:/home/gdholla1/mipav/lib/hyperapplet.jar:/home/gdholla1/mipav/lib/jaxb-api.jar:/home/gdholla1/mipav/lib/fitbir-model.jar:/home/gdholla1/mipav/lib/jhall.jar:/home/gdholla1/mipav/lib/stax-ex.jar:/home/gdholla1/mipav/lib/WildMagic.jar:/home/gdholla1/mipav/lib/camino.jar:/home/gdholla1/mipav/lib/jaxb-impl.jar:/home/gdholla1/mipav/lib/jTEM.jar:/home/gdholla1/mipav/lib/activation.jar:/home/gdholla1/mipav/lib/saaj-impl.jar:/home/gdholla1/mipav/lib/JimiProClasses.jar:/home/gdholla1/mipav/lib/tar.jar:/home/gdholla1/mipav/lib/fontbox-1.2.0.jar:/home/gdholla1/mipav/lib/log4j-1.2.16.jar:/home/gdholla1/mipav/lib/dataDictionaryClient-4.1.1.8.jar:/home/gdholla1/mipav/lib/streambuffer.jar:/home/gdholla1/mipav/lib/jaxws-rt.jar:/home/gdholla1/mipav/lib/ij.jar:/home/gdholla1/mipav/lib/jax-qname.jar:/home/gdholla1/mipav/lib/gmbal-api-only.jar:/home/gdholla1/mipav/lib/javac.jar:/home/gdholla1/mipav/lib/pdfbox-1.2.0.jar:/home/gdholla1/mipav/lib/jempbox-1.2.0.jar:/home/gdholla1/mipav/lib/fitbir-web-service.jar:/home/gdholla1/mipav/lib/ACCESSION_client_VTool.jar:/home/gdholla1/mipav/lib/junit-4.4.jar:/home/gdholla1/mipav/jre/lib/resources.jar:/home/gdholla1/mipav/jre/lib/charsets.jar:/home/gdholla1/mipav/jre/lib/alt-rt.jar:/home/gdholla1/mipav/jre/lib/deploy.jar:/home/gdholla1/mipav/jre/lib/rt.jar:/home/gdholla1/mipav/jre/lib/jsse.jar:/home/gdholla1/mipav/jre/lib/jce.jar:/home/gdholla1/mipav/jre/lib/management-agent.jar:/home/gdholla1/mipav/jre/lib/alt-string.jar:/home/gdholla1/mipav/jre/lib/javaws.jar:/home/gdholla1/mipav/jre/lib/ext/jogl.all-mobile.jar:/home/gdholla1/mipav/jre/lib/ext/joal-test.jar:/home/gdholla1/mipav/jre/lib/ext/newt.event.jar:/home/gdholla1/mipav/jre/lib/ext/j3dcore.jar:/home/gdholla1/mipav/jre/lib/ext/sunjce_provider.jar:/home/gdholla1/mipav/jre/lib/ext/jogl.all-noawt.jar:/home/gdholla1/mipav/jre/lib/ext/customizer.jar:/home/gdholla1/mipav/jre/lib/ext/multiplayer.jar:/home/gdholla1/mipav/jre/lib/ext/jhdfobj.jar:/home/gdholla1/mipav/jre/lib/ext/gluegen.jar:/home/gdholla1/mipav/jre/lib/ext/gluegen-rt.jar:/home/gdholla1/mipav/jre/lib/ext/jocl.jar:/home/gdholla1/mipav/jre/lib/ext/joal.jar:/home/gdholla1/mipav/jre/lib/ext/vecmath.jar:/home/gdholla1/mipav/jre/lib/ext/JOCL-0.1.7.jar:/home/gdholla1/mipav/jre/lib/ext/mediaplayer.jar:/home/gdholla1/mipav/jre/lib/ext/jhdf5obj.jar:/home/gdholla1/mipav/jre/lib/ext/jogl.all.jar:/home/gdholla1/mipav/jre/lib/ext/jogl.test.jar:/home/gdholla1/mipav/jre/lib/ext/sunpkcs11.jar:/home/gdholla1/mipav/jre/lib/ext/j3dutils.jar:/home/gdholla1/mipav/jre/lib/ext/jmf.jar:/home/gdholla1/mipav/jre/lib/ext/jhdf5.jar:/home/gdholla1/mipav/jre/lib/ext/dnsns.jar:/home/gdholla1/mipav/jre/lib/ext/localedata.jar:/home/gdholla1/mipav/jre/lib/im/thaiim.jar:/home/gdholla1/mipav/jre/lib/im/indicim.jar:/home/gdholla1/mipav/jre/lib/security/local_policy.jar:/home/gdholla1/mipav/jre/lib/security/US_export_policy.jar:/home/gdholla1/mipav/jre/lib/plugin.jar:/home/gdholla1/mipav/plugins/methods/methods.jar:/home/gdholla1/mipav/plugins/library/nativewindow.all.jar:/home/gdholla1/mipav/plugins/library/gluegen-rt.jar:/home/gdholla1/mipav/plugins/library/jogl.all.jar:/home/gdholla1/mipav/help/mipav_help.jar:/home/gdholla1/mipav/lax.jar:/home/gdholla1/mipav/InsightToolkit/lib/InsightToolkit/InsightToolkit.jar edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping --inFilter /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii --inInv2 /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii --inT1weighted /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii --outMasked /home/gdholla1/notebooks/outMasked.nii -xMaxProcess 1 Standard output: cli #################################################################### cli Initializing MIPAV/JIST Framework MIPAV STARTED with forceQuite set as true cli #################################################################### cli Interpretting command line arguments cli #################################################################### de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping outExecution = <default> = inSkip = <default> = false inFilter = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S7_mp2rage_whole_brain_UNI_Images.nii outMasked2 = <default> = Masked T1-weighted Image inInv2 = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S4_mp2rage_whole_brain_INV2.nii inT1weighted = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii = /home/gdholla1/data/leipzig/mri/KP6T/session1_zoomed_in/S6_mp2rage_whole_brain_T1_Images.nii outBrain = <default> = Brain Mask Image outMasked3 = <default> = Masked Filter Image inT1 = <default> = T1 Map Image outMasked = /home/gdholla1/notebooks/outMasked.nii = /home/gdholla1/notebooks/outMasked.nii outProc = /home/gdholla1/notebooks outResult = output.txt cli #################################################################### edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 0New image:256x256x176x1 edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 1New image:256x256x176x1 edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 2New image:256x256x176x1 image range: 0.0, 1499.0 mean parameters: 0.05102058095562509 iteration 1 mean parameters: 0.02495016508806164 diff parameters: 0.026070415867563448 iteration 2 mean parameters: 0.013559674465951167 diff parameters: 0.011390490622110474 iteration 3 mean parameters: 0.009698280057654995 diff parameters: 0.003861394408296172 iteration 4 mean parameters: 0.008623307046790124 diff parameters: 0.0010749730108648714 iteration 5 mean parameters: 0.008308390993678324 diff parameters: 3.1491605311179983E-4 iteration 6 mean parameters: 0.008212212609716494 diff parameters: 9.617838396182993E-5 background-based skull strippingimage: [4.9592734E-5, 0.9918051] scaled dimensions: 16 x 16 x 11 min obj size: 2816 max obj size: 278 rng obj size: 1886 and obj size: 278 main obj size: 280 boundary size: 228 scaled dimensions: 32 x 32 x 22 scaled dimensions: 64 x 64 x 44 edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 2Free image:S7_mp2rage_whole_brain_UNI_Images edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 1Free image:S6_mp2rage_whole_brain_T1_Images edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 0Free image:S4_mp2rage_whole_brain_INV2 scaled dimensions: 128 x 128 x 88 region size: 2049984 LUT loaded from: file:/home/gdholla1/mipav/plugins/de/mpg/cbs/structures/critical66LUT.raw.gz initialization fast marching init init done GDM forces: 0.0 (field), 0.1 (balloon), 0.9 (smoothing) LUT loaded from: file:/home/gdholla1/mipav/plugins/de/mpg/cbs/structures/critical66LUT.raw.gz initial GDM decomposition fast marching init done initialization level set evolution: narrow band init (1353272) iteration 0 changed labels: 3234 iteration 1 changed labels: 9607 iteration 2 changed labels: 4562 iteration 3 changed labels: 4510 iteration 4 changed labels: 4428 iteration 5 changed labels: 4019 iteration 6 changed labels: 4216 iteration 7 changed labels: 4088 iteration 8 changed labels: 4044 iteration 9 changed labels: 4412 iteration 10 changed labels: 4390 iteration 11 changed labels: 4545 iteration 12 changed labels: 5858 iteration 13 changed labels: 5455 iteration 14 changed labels: 4392 iteration 15 changed labels: 4154 iteration 16 changed labels: 3861 iteration 17 changed labels: 3517 iteration 18 changed labels: 3299 iteration 19 changed labels: 3231 iteration 20 changed labels: 3073 iteration 21 changed labels: 3147 iteration 22 changed labels: 2968 iteration 23 changed labels: 2981 iteration 24 changed labels: 3144 iteration 25 changed labels: 3022 iteration 26 changed labels: 3115 iteration 27 changed labels: 2965 iteration 28 changed labels: 2986 iteration 29 changed labels: 2991 iteration 30 changed labels: 2999 iteration 31 changed labels: 3187 iteration 32 changed labels: 2998 iteration 33 changed labels: 3157 iteration 34 changed labels: 3112 iteration 35 changed labels: 3187 iteration 36 changed labels: 3176 iteration 37 changed labels: 3071 iteration 38 changed labels: 3225 iteration 39 changed labels: 3355 iteration 40 changed labels: 3281 iteration 41 changed labels: 3256 iteration 42 changed labels: 3400 iteration 43 changed labels: 3148 iteration 44 changed labels: 3305 iteration 45 changed labels: 3253 iteration 46 changed labels: 3149 iteration 47 changed labels: 3195 iteration 48 changed labels: 3198 iteration 49 changed labels: 3116 iteration 50 changed labels: 3155 iteration 51 changed labels: 3109 iteration 52 changed labels: 3148 iteration 53 changed labels: 3123 iteration 54 changed labels: 3120 iteration 55 changed labels: 3091 iteration 56 changed labels: 3051 iteration 57 changed labels: 3168 iteration 58 changed labels: 3182 iteration 59 changed labels: 3228 iteration 60 changed labels: 3258 iteration 61 changed labels: 3284 iteration 62 changed labels: 3222 iteration 63 changed labels: 3125 iteration 64 changed labels: 3199 iteration 65 changed labels: 3183 iteration 66 changed labels: 3151 iteration 67 changed labels: 3162 iteration 68 changed labels: 3280 iteration 69 changed labels: 3210 iteration 70 changed labels: 3249 iteration 71 changed labels: 3224 iteration 72 changed labels: 3280 iteration 73 changed labels: 3284 iteration 74 changed labels: 3360 iteration 75 changed labels: 3194 iteration 76 changed labels: 3254 iteration 77 changed labels: 3362 iteration 78 changed labels: 3461 iteration 79 changed labels: 3372 iteration 80 changed labels: 3317 iteration 81 changed labels: 3318 iteration 82 changed labels: 3350 iteration 83 changed labels: 3377 iteration 84 changed labels: 3318 iteration 85 changed labels: 3433 re-initialization level set evolution: iso-surface reinit fast marching init done iteration 86 changed labels: 3738 iteration 87 changed labels: 3133 iteration 88 changed labels: 3383 iteration 89 changed labels: 3400 iteration 90 changed labels: 3305 iteration 91 changed labels: 3291 iteration 92 changed labels: 3435 iteration 93 changed labels: 3347 iteration 94 changed labels: 3542 iteration 95 changed labels: 3485 iteration 96 changed labels: 3508 iteration 97 changed labels: 3447 iteration 98 changed labels: 3468 iteration 99 changed labels: 3497 edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 0New image:256x256x176x0 edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat ImageDataFloat: 1New image:256x256x176x0 ---------- Performance Summary ---------- 1) Algorithm Calculation -- ELAPSED TIME: Actual: 1 min 7.17 sec / CPU: 1 min 6.65 sec TOTAL ELAPSED TIME: Actual: 1 min 7.17 sec / CPU: 1 min 6.65 sec CURRENT MEMORY: Used 1073 MB, Free 1359 MB, Total 2433 MB jist.io FileReaderWriter: write file:outMasked.nii cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] -help cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] [run options] cli PARSE Error: null Standard error: Could not find library, using working directory /home/gdholla1/jist-lib edu.jhu.ece.iacl.jist.pipeline.CalculationMonitorCalculation Monitor not running. Punting stop. edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher stopping via interrupt. edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher finished. java.io.IOException: NIFTI header file error at gov.nih.mipav.model.file.FileNIFTI.readImage(FileNIFTI.java:2615) at gov.nih.mipav.model.file.FileIO.readNIFTI(FileIO.java:8632) at gov.nih.mipav.model.file.FileIO.readImage(FileIO.java:2449) at gov.nih.mipav.model.file.FileIO.readImage(FileIO.java:2013) at edu.jhu.ece.iacl.jist.io.ModelImageReaderWriter.readQuiet(ModelImageReaderWriter.java:116) at edu.jhu.ece.iacl.jist.io.ModelImageReaderWriter.readObject(ModelImageReaderWriter.java:84) at edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter.readObject(ImageDataReaderWriter.java:90) at edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter.readObject(ImageDataReaderWriter.java:34) at edu.jhu.ece.iacl.jist.io.FileReaderWriter.read(FileReaderWriter.java:69) at edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume.getImageData(ParamVolume.java:480) at edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume.getImageData(ParamVolume.java:469) at edu.jhu.ece.iacl.jist.cli.run.main(run.java:122) FAILED to Open Volume from Disk: /home/gdholla1/notebooks/outMasked.nii java.lang.NullPointerException at edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav.createModelImage(ImageDataMipav.java:348) at edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter.writeObject(ImageDataReaderWriter.java:281) at edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter.writeObject(ImageDataReaderWriter.java:34) at edu.jhu.ece.iacl.jist.io.FileReaderWriter.write(FileReaderWriter.java:102) at edu.jhu.ece.iacl.jist.cli.run.main(run.java:122) Return code: 255 Interface JistBrainMp2rageSkullStripping failed to run.