Oz T1 only sample failures

Four datasets are failing for the same reason. All fail in BCD with need to pick eyes. Trouble is not in picking eyes but saving output eyes in correct format and then getting BRAINSTools to run past this? I did the usual fixes of ensuring input dataset was 1x1x1 and cropping out anything in the background and neck to no avail.

Example Failure

[cortex:singleSession_S104_S104-v1/LandmarkInitialize/BCD] axelsone% cat /Shared/nopoulos/structural/oz_MR/BAWEXPERIMENT_20180329/20180329_OZ_base_CACHE/singleSession_S104_S104-v1/LandmarkInitialize/BCD/BCD_FAILED.txt

itk::ExceptionObject (0x7b07b00) Location: "unknown" File: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-intel/BRAINSTools/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx Line: 1475 Description: itk::ERROR: EMSP aligned image and zero eye centers landmarks are written to ./. Use GUI corrector to correct the landmarks in.EMSP.fcsvINITIAL LMKS: EMSP.fcsvFOR IMAGE: Image (0x7b08790) RTTI typeinfo: itk::Image<short, 3u> Reference Count: 2 Modified Time: 12892440 Debug: Off Object Name: Observers: none Source: (none) Source output name: (none) Release Data: Off Data Released: False Global Release Data: Off PipelineMTime: 12892430 UpdateMTime: 12892439 RealTimeStamp: 0 seconds LargestPossibleRegion: Dimension: 3 Index: [0, 0, 0] Size: [256, 256, 256] BufferedRegion: Dimension: 3 Index: [0, 0, 0] Size: [256, 256, 256] RequestedRegion: Dimension: 3 Index: [0, 0, 0] Size: [256, 256, 256] Spacing: [1, 1, 1] Origin: [-127.5, -127.5, -127.5] Direction: 1 0 0 0 1 0 0 0 1

IndexToPointMatrix: 1 0 0 0 1 0 0 0 1

PointToIndexMatrix: 1 0 0 0 1 0 0 0 1

Inverse Direction: 1 0 0 0 1 0 0 0 1

PixelContainer: ImportImageContainer (0x7b07b90) RTTI typeinfo: itk::ImportImageContainer<unsigned long, short> Reference Count: 1 Modified Time: 12892437 Debug: Off Object Name: Observers: none Pointer: 0x7b110d0 Container manages memory: true Size: 16777216 Capacity: 16777216 IN DIR: ./

Description by Ali

Does not help since newer slicer doesn't save out *fscv files and what does "Changed EMSP.fcsv to have proper format" mean?

https://apps.icts.uiowa.edu/jira/browse/PREDICTIMG-3811

Case # 3:

For those cases that BCD could estimate a good MSP image: A- I Loaded EMSP.nrrd, EMSP.fcsv files by Slicer and define eyes. B- Changed EMSP.fcsv to have proper format. C- Renamed the EMSP.nrrd to "${SUBJECT}_maneyes_denoised.nrrd". D- Created the following file adjacent to the nrrd file to indicates that denoising should be skipped: touch ${SUBJECT}_maneyes_denoised.nrrd_noDenoise

Six datasets:

/Shared/nopoulos/structural/oz_MR/BAWEXPERIMENT_20180329/20180329_OZ_base_CACHE/singleSession_S104_S104-v1/LandmarkInitialize/BCD /Shared/nopoulos/structural/oz_MR/BAWEXPERIMENT_20180329/20180329_OZ_base_CACHE/singleSession_S105_S105-v1/LandmarkInitialize/BCD /Shared/nopoulos/structural/oz_MR/BAWEXPERIMENT_20180329/20180329_OZ_base_CACHE/singleSession_S106_S106-v1/LandmarkInitialize/BCD /Shared/nopoulos/structural/oz_MR/BAWEXPERIMENT_20180329/20180329_OZ_base_CACHE/singleSession_S101_S101-v1/LandmarkInitialize/BCD /Shared/nopoulos/structural/oz_MR/BAWEXPERIMENT_20180329/20180329_OZ_base_CACHE/singleSession_C004_C004-v1/LandmarkInitialize/BCD /Shared/nopoulos/structural/oz_MR/BAWEXPERIMENT_20180329/20180329_OZ_base_CACHE/singleSession_C002_C002-v1/LandmarkInitialize/BCD

NOTE One T1/T2 dataset needs same fix

I did the usual fixes of ensuring input dataset was 1x1x1 and cropping out anything in the background and neck to no avail. /Shared/hothlab/structural/MR/BAWEXPERIMENT_20180509/20180425_HOTH_base_CACHE/singleSession_D006_64428017/LandmarkInitialize/BCD