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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
BCD runs and outputs EMSP.nrrd and EMSP.fcsv files but outputs just very poor (not standard eye center issues):
/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
/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