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Two failures on GLASGOW DM1 sample
I am getting two failures on a sample of T1/T2 datasets from Glasgow Scotland. One is the familiar BCD failure where the resulting EMSP.nrrd is just really bad. This is same failure we were getting for Denburg sample examples 4-8 (BCD runs and outputs EMSP.nrrd and EMSP.fcsv files but outputs just very poor (not standard eye center issues):) The second failure is a new one that happens in BRAINSABC that I have not seen before. Both are documented below. NOTE Fixed both of these cases successfully
BCD runs and outputs EMSP.nrrd and EMSP.fcsv files but outputs just very poor (not standard eye center issues): FIXED this by cropping out anything far outside the brain. Had some ringing and white noise far outside the brain that was causing failure
/Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/singleSession_030_030-1/LandmarkInitialize/BCD/EMSP.nrrd
itk::ExceptionObject (0xfaa0a50) Location: "unknown" File: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-intel/BRAINSTools/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx Line: 1475 Description: itk::ERROR: Eyes are out of range in MSP aligned space. Normally in left-right direction, 15<LE< 45 and -45<RE<-15 LE[0] = -0.380592, RE[0] = -35.6022
/Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSConstellationDetector --LLSModel /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/Atlas/20141004_BCD/LLSModel_50Lmks.h5 --acLowerBound 80.000000 --atlasLandmarkWeights /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/Atlas/20141004_BCD/template_weights_50Lmks.wts --atlasLandmarks /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/Atlas/20141004_BCD/template_landmarks_50Lmks.fcsv --houghEyeDetectorMode 1 --inputTemplateModel /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/Atlas/20141004_BCD/T1_50Lmks.mdl --inputVolume /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/singleSession_030_030-1/N4BFC/mapflow/_N4BFC0/030_T1_clipped_N4_BFC.nii.gz --interpolationMode Linear --outputLandmarksInACPCAlignedSpace BCD_ACPC_Landmarks.fcsv --outputLandmarksInInputSpace BCD_Original.fcsv --outputResampledVolume BCD_ACPC.nii.gz --outputTransform BCD_Original2ACPC_transform.h5 --writeBranded2DImage BCD_Branded2DQCimage.png
BRAINSABC Failure regarding Infinite loop detected for auto-correction ** FIXED by changing voxel dimensions to 1x1x1**
/Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/singleSession_052_052-1/TissueClassify/BABC
ERROR: Infinite loop detected for auto-correction Check input images to ensure proper intializaiton was completed. Standard error: STATUS: Atlas image of type: T1 added with filename: /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/Atlas/template_t1_denoised_gaussian.nii.gz STATUS: Atlas image of type: T2 added with filename: /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/Atlas/template_t2_denoised_gaussian.nii.gz maskInferiorCutOffFromCenter is 65 Finshed SyN stage Before RescaleFunctionLocal Return code: 255 Interface BRAINSABCext failed to run.
/Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSABC --atlasDefinition /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/Atlas/ExtendedAtlasDefinition.xml --atlasToSubjectTransform atlas_to_subject.h5 --atlasToSubjectTransformType SyN --debuglevel 0 --filterIteration 3 --filterMethod None --inputVolumeTypes T1,T2 --inputVolumes /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/singleSession_052_052-1/LandmarkInitialize/BROIAuto_cropped/Cropped_BCD_ACPC_Aligned.nii.gz --inputVolumes /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/singleSession_052_052-1/N4BFC/mapflow/N4BFC1/052_T2_clipped_N4_BFC.nii.gz --interpolationMode Linear --maxBiasDegree 0 --maxIterations 2 --outputDir ./ --outputDirtyLabels volume_label_seg.nii.gz --outputFormat NIFTI --outputLabels brain_label_seg.nii.gz --outputVolumes 052_T1_clipped_N4_BFC_corrected.nii.gz --outputVolumes 052_T2_clipped_N4_BFC_corrected.nii.gz --posteriorTemplate POSTERIOR%s.nii.gz --purePlugsThreshold 0.100000 --restoreState /Shared/nopoulos/structural/glasgow_MR/BAWEXPERIMENT_20180323/20180323_GLASGOW_base_CACHE/singleSession_052_052-1/TissueClassify/AtlasToSubjectANTsPreABC_SyN/SavedInternalSyNState.h5 --saveState SavedBABCInternalSyNState.h5 --useKNN
FIXED by changing voxel dimensions to 1x1x1