Fix dwi convert #315
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Fix dwi convert #315
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Allows to convert DICOM series encoded with JPEG transfer syntax. ITK only registers these in one place (ITK::DCMTKImageIO), and that is too late for DWIConvert because it uses itkDCMTKSeriesFileNames to make a file list before directly (re-)reading the files. Please see discussion: http://slicer-users.65878.n3.nabble.com/DWI-to-DTI-convertion-td4031356.html
The atlas data was not referenced properly for testing.
DCMTK needs a very new revision that includes bug fixes when compiling in C++11 mode.
Version 4.8.0 is a major update for the DWIConvert program to fix problems with DWI processing interactions between FSL and NRRD based DWI processing tools.
This patch set provides some more checking regarding the imaging sequence so that we can better identify how each images is megin written.
Nifti images can have both QForm and SForm matricies.
When converting from DICOM, and either form is sufficient
to fully understand the SCANNER_ANAT.
Prefer to use only ONE of these so that there is no
mis-interpretation.
{
//Set the qform and sfrom codes for the MetaDataDictionary.
itk::MetaDataDictionary & thisDic = img4D->GetMetaDataDictionary();
itk::EncapsulateMetaData< std::string >( thisDic, "qform_code_name", "NIFTI_XFORM_SCANNER_ANAT" );
itk::EncapsulateMetaData< std::string >( thisDic, "sform_code_name", "NIFTI_XFORM_UNKNOWN" );
}
The origin for a mosaic image was not being properly identified in the previous version of the code. After investigation, the correct computation for the origin was found. With this patch set, the T1 morphometric images and the DWI images are almost perfectly overlapped.
Make variable more descriptive, and place code in more localized conditionals to reduce the amount of logic conditionals.
m_LPSDirCos and m_NRRDSpaceDirection were possible to be out of sync. Compute GetNRRDSpaceDirection as needed, and always modify the m_LPSDirCos to represent the correct orientation of the data.
Encapsulate the writting of Nrrd file to a function so that the code is more self-contained and re-usable.
Simplifying interface now that the state of the object is completely internal to the converter class.
The DWICompare program needs to be able to compare measurement frames in both native format, and in identity measurement rotated frames of reference. The DWICompare program was also re-written to use the validator common code shared by DWIConverter and DWICompare.
Using FSL to visualize the data revealed that it had been incorrectly created. After fixing DWIConvert this test was failing because the reference test data was incorrect. When compared to dcm2niix orientation bugs were fixed and manual visualization confirmed that this new data set has correct orientations.
Converting from NHDR to FSL to NRRD needs larger tolerance for the origin to accomodate miniute numerical differences.
In order to improve conformance with other FSL based tools, DWIConvert reorganizes data when writing out FSL based files. It also re-organizes data when reading from FSL files to match historical LPS/DICOM data organization that is stored in NRRD/NHDR files. These validation scripts for orientation testing The attached scripts provide mechanisms for writing and visualizing DTI images in both Slicer and FSL to ensure that data orientation representation are consistent for tensor based analysis.
There is no need to compute the max bvalue inline.
ITK DICOM reader already computes the rows & column size of the images, so there is no need to do it again.
These are not changes, but removal of comments that do not need to be addressed.
Extract dicom information and place in NRRD headers as a means of preserving information.
When converting between different data representation (i.e. FSL vs NRRD) we need to ensure that the entire data model remains consistent. Pulling values that must change in unison into consistent single transaction events can assist with the migration between different data representations.
The slice ordering needs to be corrected based on SI orientation for both direction cosines and measurement frames! This also allows makes the math easier to follow with respect to the gradient directions and how they are represented.
Keep the main DWIConverter class free of unnecessary member vars/functions.
The measurement frame implicit representations need to be managed properly for reading/writing BVec values and storing in nhdr or .bvec files. This implicitly reads and flips FSL formatted files into Identity Dicom orientation so that round trip to/from FSL results in consistent NRRD file header definition as long as the starting NRRD file has identity measurement frame and nearly identity direction cosines.
When using a refactoring tool, std::endl was replaced by a compiler specific equivalent of std::__1::endl that is not portable across compilers. This was a mistake.
C++11 syntax needed to be removed.
Restore the --allowLossyConversion behavior for cases where the input image is not a short int image type.
The same output file name can not be used for more than one test to avoid parallel testing to pass all the time.
This was referenced Dec 11, 2016
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This is a substantial re-write and re-organzation of the DWIConvert program to provide for better organization, a central consistent data model, and extensive test suite.
The rewrite helped to identify corner cases where conversion to/from FSL was often not performed correctly.