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BCD failures on Denburg T1only sample
There were 9 datasets that were failing BCD for the /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713 experiment.
/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_Results/DENBURGREST/ND141 was successfully run by manually transforming the raw T1 to get a rough ACPC alignment using Slicer Linear Transform function and cropping neck and creating this file to start over BAW with (/nopoulos/structural/denburg_MR/REST/ND141/63738316/ANONRAW/ND141_63738316_T1_fixed.nii.gz)
The above procedure did not work on the following datasets to get them to complete BCD successfully and continue with successful BAW completion. The errors are broken down below with BCD commands that fail and error messages:
These scans do not complete BCD but error out before creation of EMSP.nrrd and EMSP.fcsv files due reflective correlation failure. Ali mentions that he has no fix for these.
/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND232_63033016/LandmarkInitialize/BCD
Error itk::ExceptionObject (0xc9444d0) Location: "unknown" File: /Shared/sinapse/sharedopt/20170302/RHEL7/NEP-11/BRAINSTools/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx Line: 793 Description: itk::ERROR: Too large MSP estimation error! reflective correlation metric is: -0.386401 Estimation of landmarks will not be reliable.
BCD Command: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSConstellationDetector --LLSModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/LLSModel_50Lmks.h5 --acLowerBound 80.000000 --atlasLandmarkWeights /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_weights_50Lmks.wts --atlasLandmarks /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_landmarks_50Lmks.fcsv --houghEyeDetectorMode 1 --inputTemplateModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/T1_50Lmks.mdl --inputVolume /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND232_63033016/N4BFC/mapflow/_N4BFC0/ND232_63033016_T1_fixed_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
/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND138_63824416/LandmarkInitialize/BCD
Error: itk::ExceptionObject (0xc68f880) Location: "unknown" File: /Shared/sinapse/sharedopt/20170302/RHEL7/NEP-11/BRAINSTools/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx Line: 793 Description: itk::ERROR: Too large MSP estimation error! reflective correlation metric is: -0.260924 Estimation of landmarks will not be reliable.
BCD Command: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSConstellationDetector --LLSModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/LLSModel_50Lmks.h5 --acLowerBound 80.000000 --atlasLandmarkWeights /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_weights_50Lmks.wts --atlasLandmarks /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_landmarks_50Lmks.fcsv --houghEyeDetectorMode 1 --inputTemplateModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/T1_50Lmks.mdl --inputVolume /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND138_63824416/N4BFC/mapflow/_N4BFC0/ND138_63824416_T1_fixed_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
/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND615_65020316/LandmarkInitialize/BCD
Error: itk::ExceptionObject (0xb31bcd0) Location: "unknown" File: /Shared/sinapse/sharedopt/20170302/RHEL7/NEP-11/BRAINSTools/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx Line: 793 Description: itk::ERROR: Too large MSP estimation error! reflective correlation metric is: -0.31918 Estimation of landmarks will not be reliable.
BCD Command: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSConstellationDetector --LLSModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/LLSModel_50Lmks.h5 --acLowerBound 80.000000 --atlasLandmarkWeights /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_weights_50Lmks.wts --atlasLandmarks /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_landmarks_50Lmks.fcsv --houghEyeDetectorMode 1 --inputTemplateModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/T1_50Lmks.mdl --inputVolume /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND615_65020316/N4BFC/mapflow/_N4BFC0/ND615_65020316_T1_fixed_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
BCD runs and outputs EMSP.nrrd and EMSP.fcsv files but outputs just very poor (not standard eye center issues):
/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND624_64527116/LandmarkInitialize/BCD/EMSP.nrrd
Error: itk::ExceptionObject (0xbe5f0f0) Location: "unknown" File: /Shared/sinapse/sharedopt/20170302/RHEL7/NEP-11/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] = 70.7141, RE[0] = 28.8422
BCD Command: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSConstellationDetector --LLSModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/LLSModel_50Lmks.h5 --acLowerBound 80.000000 --atlasLandmarkWeights /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_weights_50Lmks.wts --atlasLandmarks /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_landmarks_50Lmks.fcsv --houghEyeDetectorMode 1 --inputTemplateModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/T1_50Lmks.mdl --inputVolume /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND624_64527116/N4BFC/mapflow/_N4BFC0/ND624_64527116_T1_fixed_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
/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND653_60137217/LandmarkInitialize/BCD/EMSP.nrrd
Error: itk::ExceptionObject (0xeb22ce0) Location: "unknown" File: /Shared/sinapse/sharedopt/20170302/RHEL7/NEP-11/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] = -49.6782, RE[0] = -84.1718
BCD Command: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSConstellationDetector --LLSModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/LLSModel_50Lmks.h5 --acLowerBound 80.000000 --atlasLandmarkWeights /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_weights_50Lmks.wts --atlasLandmarks /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_landmarks_50Lmks.fcsv --houghEyeDetectorMode 1 --inputTemplateModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/T1_50Lmks.mdl --inputVolume /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND653_60137217/N4BFC/mapflow/_N4BFC0/ND653_60137217_T1_fixed_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
/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND59_64226616/LandmarkInitialize/BCD/EMSP.nrrd
Error: itk::ExceptionObject (0xbbdbf10) Location: "unknown" File: /Shared/sinapse/sharedopt/20170302/RHEL7/NEP-11/BRAINSTools/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx Line: 1475 Description: itk::ERROR: Eyes are normally lower than AC point in Superior-Inferior direction in MSP aligned space.
BCD Command: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSConstellationDetector --LLSModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/LLSModel_50Lmks.h5 --acLowerBound 80.000000 --atlasLandmarkWeights /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_weights_50Lmks.wts --atlasLandmarks /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_landmarks_50Lmks.fcsv --houghEyeDetectorMode 1 --inputTemplateModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/T1_50Lmks.mdl --inputVolume /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND59_64226616/N4BFC/mapflow/_N4BFC0/ND59_64226616_T1_fixed_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
/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND522_63795816/LandmarkInitialize/BCD/EMSP.nrrd
Error: itk::ExceptionObject (0xe8f51c0) Location: "unknown" File: /Shared/sinapse/sharedopt/20170302/RHEL7/NEP-11/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] = 72.6839, RE[0] = 22.8478
BCD Command: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSConstellationDetector --LLSModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/LLSModel_50Lmks.h5 --acLowerBound 80.000000 --atlasLandmarkWeights /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_weights_50Lmks.wts --atlasLandmarks /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_landmarks_50Lmks.fcsv --houghEyeDetectorMode 1 --inputTemplateModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/T1_50Lmks.mdl --inputVolume /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND522_63795816/N4BFC/mapflow/_N4BFC0/ND522_63795816_T1_fixed_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
/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND654_64945216/LandmarkInitialize/BCD/EMSP.nrrd
Error: itk::ExceptionObject (0xc5b6460) Location: "unknown" File: /Shared/sinapse/sharedopt/20170302/RHEL7/NEP-11/BRAINSTools/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx Line: 1475 Description: itk::ERROR: Eyes are normally lower than AC point in Superior-Inferior direction in MSP aligned space.
BCD Command: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-11/bin/BRAINSConstellationDetector --LLSModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/LLSModel_50Lmks.h5 --acLowerBound 80.000000 --atlasLandmarkWeights /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_weights_50Lmks.wts --atlasLandmarks /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/template_landmarks_50Lmks.fcsv --houghEyeDetectorMode 1 --inputTemplateModel /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/Atlas/20141004_BCD/T1_50Lmks.mdl --inputVolume /Shared/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND654_64945216/N4BFC/mapflow/_N4BFC0/ND654_64945216_T1_fixed_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