Skip to content

Pull Nifti-related fixes from upstream #3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
ihnorton wants to merge 5 commits into from
Closed

Pull Nifti-related fixes from upstream #3

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
1042214
BUG: ITK is row-major; fix NRRD output with mismatched (x,y) axis sizes
ihnorton Nov 19, 2017
b6f12e1
BUG: FSL converter should check reader status
ihnorton Nov 19, 2017
f375870
Merge pull request #356 from ihnorton/fix_mismatched_axes
hjmjohnson Nov 29, 2017
12741b3
ENH: Need to add allowLossy for file types other than short.
hjmjohnson Nov 29, 2017
c1289e6
Merge pull request #358 from BRAINSia/FixLossyConversionFailure
hjmjohnson Nov 29, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions DWIConvert/DWIConverter.cxx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -342,8 +342,8 @@ void DWIConverter::ManualWriteNRRDFile(
header << "space: " << this->GetNRRDSpaceDefinition() << "" << std::endl;

const DWIConverter::RotationMatrixType& NRRDSpaceDirection = this->GetNRRDSpaceDirection();
header << "sizes: " << this->GetCols()
<< " " << this->GetRows()
header << "sizes: " << this->GetRows()
<< " " << this->GetCols()
<< " " << this->GetSlicesPerVolume()
<< " " << this->GetNVolume() << std::endl;
header << "thicknesses: NaN NaN " << DoubleConvert(GetThickness()) << " NaN" << std::endl;
Expand Down
3 changes: 2 additions & 1 deletion DWIConvert/FSLDWIConverter.cxx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,8 @@ FSLDWIConverter::LoadFromDisk()
Volume4DType::Pointer inputVol;

// string to use as template if no bval or bvec filename is given.
ReadScalarVolume<Volume4DType>(inputVol, fslNIFTIFile, this->m_allowLossyConversion);
if (ReadScalarVolume<Volume4DType>(inputVol, fslNIFTIFile, this->m_allowLossyConversion) != EXIT_SUCCESS)
throw;
// Reorient from FSL standard format to ITK/Dicom standard format
this->m_SlicesPerVolume = inputVol->GetLargestPossibleRegion().GetSize()[2];
this->m_NVolume = inputVol->GetLargestPossibleRegion().GetSize()[3];
Expand Down
2 changes: 1 addition & 1 deletion DWIConvert/TestSuite/CMakeLists.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -480,4 +480,4 @@ ExternalData_Add_Test( ${PROJECT_NAME}FetchData NAME DWIConvertMultiShellFSITe
)
AddDataDependency(DWIConvertMultiShellFSITestSmallSize)

ExternalData_Add_Target( ${PROJECT_NAME}FetchData ) # Name of data management target
ExternalData_Add_Target( ${PROJECT_NAME}FetchData ) # Name of data management target
3 changes: 2 additions & 1 deletion DWIConvert/TestSuite/FSLMultiShellDataTest.cmake
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
# first, convert multishell FSL into Nrrd
set(command_line
${TEST_PROGRAM}
--allowLossyConversion
--inputVolume ${INPUTVOLUME}
--outputVolume ${OUTPUTVOLUME}
)
Expand Down Expand Up @@ -51,4 +52,4 @@ if(TEST_RESULT)
"Failed: Recovering bvec or bval files do not match the original FSL file")
endif()

message("Passed")
message("Passed")