Install Elastix on Macbook M3 MAX chip

[GinaC4]

Hi there,

Some colleagues and I are trying to install elastix on our new machines running macOS Sonoma 14.6 (M3 MAX chip), but we encountered some difficulties.

We first installed the ITK 5.4.0 version.

Then we downloaded the elastix source code from here: https://github.com/SuperElastix/elastix

When we tried to build elastix we got the following error:

**CMake Error at CMakeLists.txt:35 (find_package):
Could not find a configuration file for package "ITK" that is compatible
with requested version "5.4.1".

The following configuration files were considered but not accepted:

 /usr/local/lib/cmake/ITK-5.4/ITKConfig.cmake, version: 5.4.0

Configuring incomplete, errors occurred!**

We weren't able to find the ITK 5.4.1 version to download..

Any help would be appreciated.

Thank you,
Gina

[N-Dekker]

Thank you for asking, Gina.

elastix has recently (Jan 2, 2024) started using ITK 5.4.1, because of a problem we had with ITK 5.4.0. If you still want to use ITK 5.4.0, you may use an older version of elastix, for example the elastix 5.2.0 tag.

If you want to use the latest version of elastix (from the main branch of git), you may find ITK 5.4.1 at https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v5.4.1

Kind regards, Niels

[GinaC4]

Eemm, I think no. I press configure then generate. When I typer elastix -help in the command line I got the following
zsh: command not found: elastix
I installed it in usr/local so I thought it will be ok if I call it from the command line

[N-Dekker]

After CMake configure and generate, did you also build it? Which C++ compiler did you use?

[GinaC4]

From the terminal I cd elastix-build folder. Then make -j -4, then sudo make install . After I typed elastix -help I got the following:

dyld[99848]: Library not loaded: @rpath/libANNlib-5.2.1.dylib
Referenced from: <8FA43F8B-2371-3FF1-93E7-F867B85ADB78> /usr/local/bin/elastix
Reason: tried: '/usr/local/lib:/usr/local/lib/cmake/ITK-5.4/libANNlib-5.2.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib:/usr/local/lib/cmake/ITK-5.4/libANNlib-5.2.1.dylib' (no such file), '/usr/local/lib:/usr/local/lib/cmake/ITK-5.4/libANNlib-5.2.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib:/usr/local/lib/cmake/ITK-5.4/libANNlib-5.2.1.dylib' (no such file)

[N-Dekker]

Interesting 🤔 Is there any file named libANNlib-5.2.1.dylib or libANNlib-5.2.dylib on your system? Somewhere in the build directory of elastix, maybe? Or in /usr/local/bin/elastix ?

[GinaC4]

Yes, there is libANNlib-5.2.1.dylib. I created a folder named elastix-4D. Inside elastix-4D I added the elastix source code namely elastix-main and I created another folder named elastix-build. The libANNlib-5.2.1.dylib is here: /Users/ginacarts/Documents/elastix-4D/elastix-build/bin

[N-Dekker]

I think you're almost there 😃 This "Library not loaded: @rpath..." is a more common problem when developing for macOS. I think you should tell the executable (elastix) where to find libANNlib-5.2.1.dylib. Something like this (while you are in the directory of the elastix executable):

install_name_tool -add_rpath /Users/ginacarts/Documents/elastix-4D/elastix-build/bin/. elastix

But I'm not 100% sure about the exact command. I read about it on https://medium.com/@donblas/fun-with-rpath-otool-and-install-name-tool-e3e41ae86172 Hope that helps for you!

[GinaC4]

Hmm when I installed elastix on my previous mac machine I didn't have this problem... That didn't work either :/ I got the following:

error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: can't open file: elastix (No such file or directory)

[N-Dekker]

Isn't elastix in your /usr/local/bin/ directory? If so, maybe you can do:

install_name_tool -add_rpath /Users/ginacarts/Documents/elastix-4D/elastix-build/bin/. /usr/local/bin/elastix

[GinaC4]

I sent an attachment of the ccmake

[GinaC4]

I did this: install_name_tool -add_rpath /Users/ginacarts/Documents/elastix-4D/elastix-build/bin/. /usr/local/bin/elastix

But I got the following error:

error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: can't create output file: /usr/local/bin/elastix.XXXXXX (Permission denied)
fatal error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: cannot rename /usr/local/bin/elastix to /usr/local/bin/elastix.XXXXXX (No such file or directory)

[N-Dekker]

@GinaC4 Can you please try the same command again, but in administrator mode? Using sudo? I think it should be as follows:

sudo install_name_tool -add_rpath /Users/ginacarts/Documents/elastix-4D/elastix-build/bin/. /usr/local/bin/elastix

It will probably ask for your password.

---

PS For more information on loading "dylib" files on Mac, you may check a site, suggested by my colleague Baldur: https://clarkkromenaker.com/post/library-dynamic-loading-mac/

[GinaC4]

Hi Niels,

That worked, thanks a lot for your help :)