Comments (3)
This should be possible with the --target=N4BiasFieldCorrection
option in cmake
. On the other hand, this seems like a premature minimization. What if other ants functionality is added to mrtrix3 in the future? I think there are other options in the cmake
build for ants that can reduce compilation time -- mostly disabling tests, particularly the long tests.
Here is an example cmake
command for this.
git clone ants...
cd ants
mkdir build && cd build
cmake \
-DBUILD_ALL_ANTS_APPS:BOOL=OFF \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DBUILD_TESTING:BOOL=OFF \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DCMAKE_INSTALL_PREFIX:PATH=/opt/ants \
-DRUN_LONG_TESTS:BOOL=OFF \
-DRUN_SHORT_TESTS:BOOL=OFF \
--target=N4BiasFieldCorrection \
..
make
This will not build only N4BiasFieldCorrection
, though, because this program depends on other parts of the ANTs library.
from containers.
On the other hand, this seems like a premature minimization. What if other ants functionality is added to mrtrix3 in the future?
Not too concerned about this. If a script were added to MRtrix3 that utilised some other ANTs functionality, that would have to go in a minor MRtrix3 version number update, and then it would make perfect sense to push out a corresponding new base container. Though I'd prefer to be reducing the number of external software dependencies of MRtrix3 rather than increasing. Anything that's not a compulsory step in a common processing pipeline, and utilises non-MRtrix3 commands, would be better provided as a standalone MRtrix3 "module" / "project" rather than being integrated into MRtrix3 itself.
from containers.
Closed through #11.
Note that with MRtrix3/mrtrix3#2197, the set of ANTs commands that may be utilised by MRtrix3 commands will expand. The current plan is to create a dev
branch on this repo MRtrix3/containers
, which checks out the dev
branch of MRtrix3, incorporates additional command tests such that those new dependencies are detected, and can genereate minified dependency tarballs for upload to OSF; once MRtrix3 experiences a merge from dev
to master
and tag, this branch MRtrix3/containers
will also experience a merge from dev
to master, with MRtrix3_GIT_COMMITISH
reverted back to master
.
from containers.
Related Issues (11)
- Strip down external dependencies? HOT 7
- Add FreeSurfer LUT HOT 2
- Install ACPCdetect
- Check FSL scripts for branches HOT 1
- Resolving PRs #4 and #11 HOT 3
- Test / document GUI usage HOT 2
- Test building with Singularity HOT 1
- Dedicated Singularity build recipe
- Obscure external packages from container interface
- neurodocker minify fails HOT 1
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