Installation no longer works, but a solution is relatively simple

[LeeReid1]

Hiya,

Thanks for this great tool.

Installation no longer works because this version is not compatible with newer versions of eigen. Errors are reported along the lines of:

failed with output

In file included from core/mrtrix.cpp:17:
In file included from ./core/mrtrix.h:37:
./core/types.h:326:9: error: redefinition of 'Vector3' as different kind of symbol

On forums for the main mrtrix branch, Donald offers a solution, which I think would be best put into the build instructions:

# navigate to your MRtrix3Tissue installation:
cd MRtrix3Tissue

# download Eigen repo and checkout older version:
git clone https://gitlab.com/libeigen/eigen.git
cd Eigen
git checkout 3.3.9
cd ..

# try again with appropriate flags:
EIGEN_CFLAGS="-isystem $(pwd)/eigen" ./configure
./build

[turuilin]

Hi，I downloaded Eigen 3.3.9 and tried again with appropriate flags:
EIGEN_CFLAGS="-isystem /data/home/bnu006/eigen/eigen-3.3.9" ./configure -nogui. However, I encountered errors when do "./build" :

"ERROR: (187/371) [LB] bin/5tt2gmwmi g++ tmp/src/dwi/tractography/seeding/list.o tmp/src/dwi/tractography/ACT/act.o tmp/src/dwi/tractography/rng.o tmp/cmd/5tt2gmwmi.o tmp/src/dwi/tractography/roi.o tmp/src/exec_version.o -lmrtrix -Wl,--sort-common,--as-needed -pthread -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/data/home/bnu006/anaconda3/lib -Wl,-rpath-link,/data/home/bnu006/anaconda3/lib -L/data/home/bnu006/anaconda3/lib -L/data/home/bnu006/anaconda3/lib -lz -L/data/home/bnu006/anaconda3/lib -lfftw3 -Wl,-rpath,$ORIGIN/../lib -L./lib -o bin/5tt2gmwmi failed with output /data/home/bnu006/fsl/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/bnu006/anaconda3/lib/libmrtrix.so: undefined reference to memcpy@GLIBC_2.14' /data/home/bnu006/fsl/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/bnu006/anaconda3/lib/liblzma.so.5: undefined reference to clock_gettime@GLIBC_2.17' collect2: error: ld returned 1 exit status "

How can I solve these issues?

[LeeReid1]

Hi @turuilin I don't think this has anything to do with the eigen issue.... except it demonstrates that you did get the eigen part working. It looks like you're using the compiler that comes with fsl, which I believe is not supported. I would use the proper compiler that comes with your system instead.