MHD writter Format not readable by SimpleITK or 3D slicer

[waltsims]

Background information

written Beamformed (3D) mhd files are not readable by either Simple ITK or 3D Slicer.

File

ObjectType = Image
NDims = 3
DimSize = 256 2000 26        
ElementNumberOfChannels = 1
ElementType = MET_UCHAR
ElementSpacing = 0.02001000500250125005 0.02001000500250125005 1
AnatomicalOrientation = RAI
BinaryData = True
BinaryDataByteOrderMSB = False
CenterOfRotation = 0 0 0
CompressedData = False
TransformMatrix = 1 0 0 0 1 0 0 0 1
UltrasoundImageOrientation = MFA
UltrasoundImageType = BRIGHTNESS
ElementByteOrderMSB = False
Seq_Frame0000_ImageStatus = OK
Seq_Frame0000_Timestamp = 1515760436.051510096
Seq_Frame0001_ImageStatus = OK
Seq_Frame0001_Timestamp = 1515760436.626828194
Seq_Frame0002_ImageStatus = OK
Seq_Frame0002_Timestamp = 1515760437.204338074
Seq_Frame0003_ImageStatus = OK
Seq_Frame0003_Timestamp = 1515760437.782961369
Seq_Frame0004_ImageStatus = OK
Seq_Frame0004_Timestamp = 1515760438.362620831
Seq_Frame0005_ImageStatus = OK
Seq_Frame0005_Timestamp = 1515760438.941310644
Seq_Frame0006_ImageStatus = OK
Seq_Frame0006_Timestamp = 1515760439.531028748
Seq_Frame0007_ImageStatus = OK
Seq_Frame0007_Timestamp = 1515760440.108578205
Seq_Frame0008_ImageStatus = OK
Seq_Frame0008_Timestamp = 1515760440.688335657
Seq_Frame0009_ImageStatus = OK
Seq_Frame0009_Timestamp = 1515760441.269950628
Seq_Frame0010_ImageStatus = OK
Seq_Frame0010_Timestamp = 1515760441.848456621
Seq_Frame0011_ImageStatus = OK
Seq_Frame0011_Timestamp = 1515760442.428308725
Seq_Frame0012_ImageStatus = OK
Seq_Frame0012_Timestamp = 1515760443.006823063
Seq_Frame0013_ImageStatus = OK
Seq_Frame0013_Timestamp = 1515760443.585642338
Seq_Frame0014_ImageStatus = OK
Seq_Frame0014_Timestamp = 1515760444.164233446
Seq_Frame0015_ImageStatus = OK
Seq_Frame0015_Timestamp = 1515760444.742943048
Seq_Frame0016_ImageStatus = OK
Seq_Frame0016_Timestamp = 1515760445.322571278
Seq_Frame0017_ImageStatus = OK
Seq_Frame0017_Timestamp = 1515760445.902441978
Seq_Frame0018_ImageStatus = OK
Seq_Frame0018_Timestamp = 1515760446.479923725
Seq_Frame0019_ImageStatus = OK
Seq_Frame0019_Timestamp = 1515760447.072831154
Seq_Frame0020_ImageStatus = OK
Seq_Frame0020_Timestamp = 1515760447.673601389
Seq_Frame0021_ImageStatus = OK
Seq_Frame0021_Timestamp = 1515760448.252296448
Seq_Frame0022_ImageStatus = OK
Seq_Frame0022_Timestamp = 1515760448.842797518
Seq_Frame0023_ImageStatus = OK
Seq_Frame0023_Timestamp = 1515760449.629186869
Seq_Frame0024_ImageStatus = OK
Seq_Frame0024_Timestamp = 1515760450.214698553
Seq_Frame0025_ImageStatus = OK
Seq_Frame0027_Timestamp = 1515760450.801201105

3D Slicer error log:

File cannot be read: /Volumes/data/MICCAI2018_ENHANCEMENT/scan_converted_ground_truth/With_Protocoll/Guillaume_Zahnd_33_M/Right/Transverse/Thyroid/rawData_19_beamformed.mhd for reading.
Reason: Undefined error: 0


Algorithm vtkITKArchetypeImageSeriesScalarReader(0x130eae5d0) returned failure for request: vtkInformation (0x60400386d580)
  Debug: Off
  Modified Time: 3516961
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_INFORMATION
  FORWARD_DIRECTION: 0
  ALGORITHM_AFTER_FORWARD: 1




ReadData: This is not a nrrd file


ReadData: Cannot read file as a volume of type DiffusionTensorVolume[fullName = /Volumes/data/MICCAI2018_ENHANCEMENT/scan_converted_ground_truth/With_Protocoll/Guillaume_Zahnd_33_M/Right/Transverse/Thyroid/rawData_19_beamformed.mhd]
	Number of files listed in the node = 0.
	File reader says it was able to read 1 files.
	File reader used the archetype file name of /Volumes/data/MICCAI2018_ENHANCEMENT/scan_converted_ground_truth/With_Protocoll/Guillaume_Zahnd_33_M/Right/Transverse/Thyroid/rawData_19_beamformed.mhd [reader 0th file name = /Volumes/data/MICCAI2018_ENHANCEMENT/scan_converted_ground_truth/With_Protocoll/Guillaume_Zahnd_33_M/Right/Transverse/Thyroid/rawData_19_beamformed.mhd]
FileFormatError



ReadData: This is not a nrrd file


ReadData: Failed to instantiate a file reader


ReadData: Cannot read file as a volume of type Volume[fullName = /Volumes/data/MICCAI2018_ENHANCEMENT/scan_converted_ground_truth/With_Protocoll/Guillaume_Zahnd_33_M/Right/Transverse/Thyroid/rawData_19_beamformed.mhd]
	Number of files listed in the node = 0.
	File reader says it was able to read 1 files.
	File reader used the archetype file name of /Volumes/data/MICCAI2018_ENHANCEMENT/scan_converted_ground_truth/With_Protocoll/Guillaume_Zahnd_33_M/Right/Transverse/Thyroid/rawData_19_beamformed.mhd [reader 0th file name = /Volumes/data/MICCAI2018_ENHANCEMENT/scan_converted_ground_truth/With_Protocoll/Guillaume_Zahnd_33_M/Right/Transverse/Thyroid/rawData_19_beamformed.mhd]
FileFormatError

Solution:

After a comparison of past .mhd files It would seem the "ElementDataFile" tag is not being written to the end of the MHD. I have manually added the line and the file format can be loaded.

Missing line from example

ElementDataFile = rawData_6_beamformed.raw

[waltsims]

MhdSequenceWritter.cpp Line 180 is this still being called? I will do some further searching.

[waltsims]

ImageOutputDevice.cpp Line99 ->close() is called but not ->closeFiles() which so the last line is not written if I read the code correctly.