How to enable nifti2 library

lassoan · August 18, 2020, 3:25am

I would like to try using nifti2 library, but if I set USE_NIFTI2_CODE then it gets reverted to USE_NIFTI2_CODE=OFF in this line:

github.com

InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/NIFTI/src/CMakeLists.txt#L8


set(ITK_VERSION_MAJOR 5)
set(ITK3P_INSTALL_EXPORT_NAME "${ITKNIFTI-targets}")
set(ITK3P_INSTALL_INCLUDE_DIR "${ITKNIFTI_INSTALL_INCLUDE_DIR}")
set(ITK3P_INSTALL_RUNTIME_DIR "${ITKNIFTI_INSTALL_RUNTIME_DIR}")
set(ITK3P_INSTALL_LIBRARY_DIR "${ITKNIFTI_INSTALL_LIBRARY_DIR}")
set(ITK3P_INSTALL_ARCHIVE_DIR "${ITKNIFTI_INSTALL_ARCHIVE_DIR}")

set(USE_NIFTI2_CODE OFF CACHE BOOL "Do not build NIFTI2 provided by NIFTI" FORCE)
set(USE_FSL_CODE OFF CACHE BOOL "Do not build FSL provided by NIFTI" FORCE)
set(USE_CIFTI_CODE OFF  CACHE BOOL "Do not build CIFTI provided by NIFTI" FORCE)
set(USE_NIFTICDF_CODE OFF CACHE BOOL "Do not build NIFTICDF provided by NIFTI" FORCE)
set(NIFTI_USE_PACKAGING OFF CACHE BOOL "Do not use packaging from nifti when included as part of another package" FORCE)
set(NIFTI_BUILD_APPLICATIONS OFF CACHE BOOL "Do not build applications provided by NIFTI" FORCE)
# Testing is not compatible with ITK at the moment
set(NIFTI_BUILD_TESTING OFF) # "Do not build nifit testing applications"

add_definitions(-DITKZLIB)
set(NIFTI_INSTALL_EXPORT_NAME ${ITKNIFTI-targets}) # "Set the nifti package export target name"

Is this intentional?

dzenanz · August 18, 2020, 1:36pm

It it probably intentional, but @hjmjohnson could provide more information as he last updated it.

hjmjohnson · August 18, 2020, 2:11pm

@lassoan. At the time of the last update of ITK’s nifti_clib code, was unable to verify that the nifti2 support would work. I have seen recent work on on the upstream nfti_clib package to fix some deficiencies with the behaviors of nifti2, and I am unsure if they have been resolved.

I would recommend 1) verifying that nifti2 is stable in the upstream nifti_clib implementation, 2) updating ITK’s internal NIFTI with the latest upstream code, and then 3) doing your test.

This is a backburner item for me to do, but it will likely not be until next spring before I get a chance to work on it.

Hans

lassoan · August 18, 2020, 2:26pm

Thank you, I just wanted to make sure that I don’t miss something trivial. I’ve submitted an issue for the problem that I’ve been experiencing with niftilib (and you have already commented on it - thank you).