Import NRRD format

seyang · November 14, 2022, 1:22am

Someone can provide sample NRRD format for my case?
I have raw sequence images as below.
slice0000.raw , slice0001.raw , slice0002, slice0003.raw…240

I tried to load NRRD with the help of a good person, but an error occurred.

[Error]
^ vtkMRMLStorageNode::ReadData: Failed to read node slice_1 (vtkMRMLScalarVolumeNode1) from filename=‘D:/2022.09.29 CT/slice.nrrd’
^ void __cdecl qSlicerIOManager::showLoadNodesResultDialog(bool,class vtkMRMLMessageCollection *) Errors occurred while loading nodes: “Error: Loading D:/2022.09.29 CT/slice.nrrd - load failed.\n”

[Used NRRD format]
NRRD0004
type: ushort
dimension: 3
sizes: 1000 800 240
encoding: raw
data file: ./slice0000
./slice0001
./slice0002
./slice0003
./slice0004

Could you please let me know what is wrong?
It will be really helpful for me.

seyang · November 14, 2022, 2:53am

Here is detailed error message.

^ vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open D:/2022.09.29 CT/X-Plane.nhdr. ITK exception info: error in unknown: Could not create IO object for reading file D:/2022.09.29 CT/X-Plane.nhdr
^ Tried to create one of the following:
^ BMPImageIO
^ BioRadImageIO
^ DCMTKImageIO
^ GDCMImageIO
^ GiplImageIO
^ JPEGImageIO
^ LSMImageIO
^ MGHImageIO
^ MINCImageIO
^ MRCImageIO
^ MetaImageIO
^ NiftiImageIO
^ NrrdImageIO
^ PNGImageIO
^ ScancoImageIO
^ StimulateImageIO
^ TIFFImageIO
^ VTKImageIO
^ MRMLIDImageIO
^ You probably failed to set a file suffix, or
^ set the suffix to an unsupported type.
^ Algorithm vtkITKArchetypeDiffusionTensorImageReaderFile(00000141540D0BA0) returned failure for request: vtkInformation (00000141587B0120)
^ Debug: Off
^ Modified Time: 209976
^ Reference Count: 1
^ Registered Events: (none)
^ Request: REQUEST_INFORMATION
^ FORWARD_DIRECTION: 0
^ ALGORITHM_AFTER_FORWARD: 1
^ vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open D:/2022.09.29 CT/X-Plane.nhdr. ITK exception info: error in unknown: Could not create IO object for reading file D:/2022.09.29 CT/X-Plane.nhdr
^ Tried to create one of the following:
^ BMPImageIO
^ BioRadImageIO
^ DCMTKImageIO
^ GDCMImageIO
^ GiplImageIO
^ JPEGImageIO
^ LSMImageIO
^ MGHImageIO
^ MINCImageIO
^ MRCImageIO
^ MetaImageIO
^ NiftiImageIO
^ NrrdImageIO
^ PNGImageIO
^ ScancoImageIO
^ StimulateImageIO
^ TIFFImageIO
^ VTKImageIO
^ MRMLIDImageIO
^ You probably failed to set a file suffix, or
^ set the suffix to an unsupported type.
^ Algorithm vtkITKArchetypeImageSeriesVectorReaderSeries(00000141540D43E0) returned failure for request: vtkInformation (00000141587BADF0)
^ Debug: Off
^ Modified Time: 211490
^ Reference Count: 1
^ Registered Events: (none)
^ Request: REQUEST_INFORMATION
^ FORWARD_DIRECTION: 0
^ ALGORITHM_AFTER_FORWARD: 1
^ vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open D:/2022.09.29 CT/X-Plane.nhdr. ITK exception info: error in unknown: Could not create IO object for reading file D:/2022.09.29 CT/X-Plane.nhdr
^ Tried to create one of the following:
^ BMPImageIO
^ BioRadImageIO
^ DCMTKImageIO
^ GDCMImageIO
^ GiplImageIO
^ JPEGImageIO
^ LSMImageIO
^ MGHImageIO
^ MINCImageIO
^ MRCImageIO
^ MetaImageIO
^ NiftiImageIO
^ NrrdImageIO
^ PNGImageIO
^ ScancoImageIO
^ StimulateImageIO
^ TIFFImageIO
^ VTKImageIO
^ MRMLIDImageIO
^ You probably failed to set a file suffix, or
^ set the suffix to an unsupported type.
^ Algorithm vtkITKArchetypeImageSeriesVectorReaderFile(00000141540D56A0) returned failure for request: vtkInformation (00000141587B00D0)
^ Debug: Off
^ Modified Time: 211597
^ Reference Count: 1
^ Registered Events: (none)
^ Request: REQUEST_INFORMATION
^ FORWARD_DIRECTION: 0
^ ALGORITHM_AFTER_FORWARD: 1
^ vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open D:/2022.09.29 CT/X-Plane.nhdr. ITK exception info: error in unknown: Could not create IO object for reading file D:/2022.09.29 CT/X-Plane.nhdr
^ Tried to create one of the following:
^ BMPImageIO
^ BioRadImageIO
^ DCMTKImageIO
^ GDCMImageIO
^ GiplImageIO
^ JPEGImageIO
^ LSMImageIO
^ MGHImageIO
^ MINCImageIO
^ MRCImageIO
^ MetaImageIO
^ NiftiImageIO
^ NrrdImageIO
^ PNGImageIO
^ ScancoImageIO
^ StimulateImageIO
^ TIFFImageIO
^ VTKImageIO
^ MRMLIDImageIO
^ You probably failed to set a file suffix, or
^ set the suffix to an unsupported type.
^ Algorithm vtkITKArchetypeImageSeriesScalarReader(00000141540D0BA0) returned failure for request: vtkInformation (00000141587BF580)
^ Debug: Off
^ Modified Time: 212406
^ Reference Count: 1
^ Registered Events: (none)
^ Request: REQUEST_INFORMATION
^ FORWARD_DIRECTION: 0
^ ALGORITHM_AFTER_FORWARD: 1
^ vtkMRMLStorageNode::ReadData: Failed to read node X-Plane (vtkMRMLMultiVolumeNode1) from filename=‘D:/2022.09.29 CT/X-Plane.nhdr’
^ ReadData: This is not a nrrd file
^ vtkMRMLStorageNode::ReadData: Failed to read node X-Plane (vtkMRMLDiffusionWeightedVolumeNode1) from filename=‘D:/2022.09.29 CT/X-Plane.nhdr’
^ vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Cannot read file as a volume of type DiffusionTensorVolume [fullName = D:/2022.09.29 CT/X-Plane.nhdr]: FileFormatError. 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 D:/2022.09.29 CT/X-Plane.nhdr [reader 0th file name = D:/2022.09.29 CT/X-Plane.nhdr].
^ vtkMRMLStorageNode::ReadData: Failed to read node X-Plane (vtkMRMLDiffusionTensorVolumeNode1) from filename=‘D:/2022.09.29 CT/X-Plane.nhdr’
^ ReadData: This is not a nrrd file
^ vtkMRMLStorageNode::ReadData: Failed to read node X-Plane (vtkMRMLVectorVolumeNode1) from filename=‘D:/2022.09.29 CT/X-Plane.nhdr’
^ vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Failed to instantiate a file reader
^ vtkMRMLStorageNode::ReadData: Failed to read node X-Plane (vtkMRMLVectorVolumeNode2) from filename=‘D:/2022.09.29 CT/X-Plane.nhdr’
^ vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Cannot read file as a volume of type Volume [fullName = D:/2022.09.29 CT/X-Plane.nhdr]: FileFormatError. 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 D:/2022.09.29 CT/X-Plane.nhdr [reader 0th file name = D:/2022.09.29 CT/X-Plane.nhdr].
^ vtkMRMLStorageNode::ReadData: Failed to read node X-Plane (vtkMRMLScalarVolumeNode1) from filename=‘D:/2022.09.29 CT/X-Plane.nhdr’
^ void __cdecl qSlicerIOManager::showLoadNodesResultDialog(bool,class vtkMRMLMessageCollection *) Errors occurred while loading nodes: “Error: Loading D:/2022.09.29 CT/X-Plane.nhdr - load failed.\n”

lassoan · November 14, 2022, 8:37pm

I’ve just tried this and it works flawlessly.

I’ve used this MRHead.nhdr file:

NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: unsigned short
dimension: 3
space: left-posterior-superior
sizes: 256 256 130
space directions: (0,1,0) (0,0,-1) (-1.2999954223632812,0,0)
kinds: domain domain domain
endian: little
encoding: raw
space origin: (86.644897460937486,-133.92860412597656,116.78569793701172)
data file: MRHead%04d.raw 0 129 1

with filenames:

MRHead0000.raw
MRHead0001.raw
MRHead0002.raw
…
MRHead0129.raw

All the files can be downloaded from here.

seyang · November 15, 2022, 4:21am

Thanks lassoan.

For your advice, i found solution with someone helping.

lassoan · November 15, 2022, 12:16pm

Could you describe what was the problem and how you solved it (just to help the next person who may run into the same difficulty)? Thank you!

seyang · November 18, 2022, 6:36am

Hi, I edited text to use your attached nhdr file by notpad.
After editing text, it require “Enter” key one by one.
If i didn’t it, the error message occurs with [This is not Nhdr file]

NRRD0004 [Enter]
type: unsigned short [Enter]
dimension: 3 [Enter]
space: left-posterior-superior [Enter]
sizes: 1000 800 240 [Enter]
space directions: (0.0277307,0,0) (0,0.0277307,0) (0,0,0.0277307) [Enter]
endian: little [Enter]
encoding: raw [Enter]
datafile: slice%04d.raw 0 239 1 [Enter]

In additionally, i made .bat file. It can make NHDR file to refer original text file.

https://humantek-my.sharepoint.com/:u:/g/personal/sykim_humantek_onmicrosoft_com/Ect3zZ9xFAdLpWdJEB9SlXABAIERAnopIY8j7SYOK9xb9w?e=9DoETe

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Import NRRD format

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