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.

Fixed: /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)

Continued Failures: 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:

Reflective Correlation Failures: These scans do not complete BCD but error out before creation of EMSP.nrrd and EMSP.fcsv files due reflective correlation failure

Dataset1: /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

Dataset 2: /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 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. /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

/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND624_64527116/LandmarkInitialize/BCD/EMSP.nrrd 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 /nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND653_60137217/LandmarkInitialize/BCD/EMSP.nrrd 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 /nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND59_64226616/LandmarkInitialize/BCD/EMSP.nrrd 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. /nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND522_63795816/LandmarkInitialize/BCD/EMSP.nrrd 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

/nopoulos/structural/denburg_MR/REST/BAWEXPERIMENT_20170713/20170302_DENBURGREST_base_CACHE/singleSession_ND654_64945216/LandmarkInitialize/BCD

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.