MRtrix3Tissue installation error

[math_priyanka]

When i am trying to install MRTris3Tissue, i am getting this error. is this beacuse of path of anaconda?

MRtrix3Tissue build type requested: release version

MRtrix3Tissue is a fork of the MRtrix3 project

Detecting OS: linux
Looking for compiler [/home/pc/fsl/bin/x86_64-conda-linux-gnu-c++]: x86_64-conda-linux-gnu-c++ (conda-forge gcc 12.3.0-2) 12.3.0
Checking for C++11 compliance: test failed (see configure.log for details)


ERROR: no suitable compiler found!



  Set the CXX environment variable to inform 'configure' of the path to the
  compiler on your system, as follows:
    $ export CXX=/usr/bin/g++-5.5
    $./configure
  (amend with the actual path to the compiler on your system)

  If you are using a compiler other than gcc or clang, you can also set the CXX_ARGS
  environment variable to specify how your compiler expects different arguments
  to be presented on the command line, for instance as follows:
    $ export CXX_ARGS="-c CFLAGS SRC -o OBJECT"
    $ ./configure


  See the file 'configure.log' for details. MRtrix3Tissue is a fork of the
  MRtrix3 project. The functionality of the configure script is unmodified,
  so when experiencing problems with this script, you might be able to find
  assistance in the MRtrix3 community forum at http://community.mrtrix.org/.
  Make sure to include the full contents of the 'configure.log' file to
  enable community members to help you efficiently. If you believe there are
  bugs or other issues with the script, it might be useful to flag these to
  MRtrix3 developers as well, as bug fixes are likely to be useful to both
  MRtrix3 and MRtrix3Tissue.

[math_priyanka]

I uninstall anaconda then /.configuration file run fine. but ./build command did not run

(base) pc@pc-HP-Pavilion-Laptop-14-dv1xxx:~/MRtrix3Tissue$ ./build
( 1/506) [CC] tmp/src/connectome/lut.o
( 2/506) [CC] tmp/core/math/average_space.o
( 3/506) [CC] tmp/core/stats.o
( 4/506) [CC] tmp/core/file/dicom/quick_scan.o
( 5/506) [CC] tmp/core/file/dicom/patient.o
( 6/506) [CC] tmp/core/image_io/gz.o
( 7/506) [CC] tmp/core/formats/png.o
( 8/506) [CC] tmp/core/image_io/variable_scaling.o

ERROR: ( 3/506) [CC] tmp/core/stats.o

clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE=“release version” -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_TIFF_SUPPORT -DMRTRIX_PNG_SUPPORT -DEIGEN_FFTW_DEFAULT -Wall -O3 -DNDEBUG -Isrc -I./core -Icmd -idirafter /usr/include/eigen3 -DEIGEN_DONT_PARALLELIZE core/stats.cpp -o tmp/core/stats.o

failed with output

In file included from core/stats.cpp:17:
In file included from ./core/stats.h:21:
In file included from ./core/app.h:28:
In file included from ./core/cmdline_option.h:28:
In file included from ./core/mrtrix.h:37:

what should i do
.

[jdtournier]

Hi @math_priyanka,

Yes, that would most likely be due to anaconda being in your path. We’ve noticed recent installs of FSL come bundled with their own miniconda environment, and if you’re not careful, that will end up in your own PATH. We typically try to deal with the presence of conda-related entries in the PATH, but this works by detecting the presence of conda in the folder name somewhere – which isn’t the case with the FSL-supplied version. So our own attempts at avoiding the issue don’t work here.

Nonetheless, the presence of the FSL-supplied anaconda compiler in your PATH indicates that your FSL install isn’t quite right. What the FSL devs have done is to put their FSL commands, which were in $FSLDIR/bin, into $FSLDIR/share/fsl/bin, and put the full miniconda environment into $FSLDIR/bin. This means that adding $FSLDIR/bin to your PATH manually (which is what we all used to do…) immediately causes (a lot of) conflicts – and not just with MRtrix3!

The right way to set up FSL (if installed using their fslinstaller script) is just to set the $FSLDIR environment variable, and run the appropriate shell config script. On my system, in the BASH shell, this looks like:

export FSLDIR=/opt/fsl
. "${FSLDIR}"/etc/fslconf/fsl.sh

In other words, do not manually modify your PATH to include $FSLDIR/bin – let the fslconf script do that for you, and that should work for all versions of FSL…

So to cut a long story short, look into your shell startup scripts (~/.bashrc, ~/.profile, or maybe ~/.cshrc, ~/.tcshrc, ~/.zshrc, … depending on what shell you use…) and locate where FSL is being set up, make sure you remove the bit that manually modifies the PATH, and copy/paste the instructions above (they may need to be modified for different shells – the above should work for sh, bash and zsh). Once that’s done, restart your terminal, and check that your PATH does not include $FSLDIR/bin (using e.g. echo $PATH). If this all checks out, the MRtrix3 (or MRtrix3Tissue) install should work correctly.

Hope this helps…
Donald.

---

For completeness, this is the relevant comment within my own copy of $FSLDIR/etc/fslconf/fsl.sh (lines 17-31):

# If this is an official (fslinstaller-installed) FSL
# installation, wrappers to FSL executables will have
# been created in $FSLDIR/share/fsl/bin/ We add this to
# the $PATH, rather than adding $FSLDIR/bin/ to the
# path, to avoid clobbering the user's environment with
# other executalbes that have been installed into
# $FSLDIR/bin/ (e.g.  python).
#
# The fslinstaller creates a file called
# $FSLDIR/etc/fslversion when it installs official FSL
# installations.
#
# If this is a manually managed installation, it is the
# user's responsibility to add $FSLDIR/bin to the $PATH

[math_priyanka]

I’m relatively novice to Ubuntu core commands, and I encountered confusion regarding the FSL installation. It appears that the presence of $FSLDIR/bin in the $PATH is causing conflicts. Right?

CUrrently, FSL installed in /home/pc/fsl

pc@pc-HP-Pavilion-Laptop-14-dv1xxx:/$ echo $FSLDIR
/home/pc/fsl

So I chnaged the PATH in ~/.bashrc , ~/.profile as

export FSLDIR=/home/pc/fsl
. "${FSLDIR}"/etc/fslconf/fsl.sh

(did not find anything in ~/.cshrc , ~/.tcshrc , ~/.zshrc )

Should I reinstall FSL and chnaged the installation directory to /opt/fsl??

Other thing,
I tried to remove the $FSLDIR/bin , but unable to do that

pc@pc-HP-Pavilion-Laptop-14-dv1xxx:~/Documents/research/data$ echo $PATH
/home/pc/fsl/share/fsl/bin:/home/pc/ANTs/bin:/home/pc/mrtrix3/bin:/home/pc/freesurfer/bin:/home/pc/freesurfer/fsfast/bin:/home/pc/freesurfer/tktools:/home/pc/fsl/bin:/home/pc/fsl/share/fsl/bin:/home/pc/freesurfer/mni/bin:/home/pc/fsl/share/fsl/bin:/home/pc/fsl/share/fsl/bin:/home/pc/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin

I have checked all ~/.bashrc , ~/.profile , ~/.cshrc , ~/.tcshrc , ~/.zshrc, but can’t remove ‘/home/pc/fsl/share/fsl/bin’; ‘/home/pc/fsl/bin’

[jdtournier]

@math_priyanka

Should I reinstall FSL and chnaged the installation directory to /opt/fsl??

No, it’s a really simple issue to fix, you don’t need to re-install everything!

@math_priyanka

It appears that the presence of $FSLDIR/bin in the $PATH is causing conflicts. Right?

That’s basically the problem, yes.

I have to acknowledge that working out where the different bits of the PATH are set can be really confusing – there are some conventions, but people and projects often come up with all sorts of different solutions, which does not make it easy to figure this out…

First thing is to confirm what shell you are using:

echo $SHELL

I’m assuming you are using the bash shell, in which case I expect the output to be /bin/bash

Assuming that’s the case, you can try to pull out all lines in the likely files that mention the PATH

grep PATH ~/.bashrc ~/.profile ~/.bash_aliases ~/.login ~/.bash_login ~/.bash_profile /etc/profile /etc/bash.bashrc /etc/environment /etc/profile.d/*

I’ve listed pretty much every file I can possibly think of, but it’s always possible that some of your startup scripts actually themselves decide to invoke some other file I haven’t thought of. But hopefully that will allow you to identify the file where /home/pc/fsl/bin (or ~/fsl/bin) is added to your PATH…

By the way, I note this is likely to be happening in several places, since I can see 4 separate occurrences of /home/pc/fsl/share/fsl/bin in your PATH – you only need to include it once, and it’s typically best done in the ~/.bashrc – though you’ll find different people will give different advice on that front…

In desperation, we can run this little snippet of code (from StackOverflow) to list all the files that your shell reads when it starts. If you post the output, we might be able to identify files that we hadn’t thought of…

echo exit | strace bash -li |& grep '^open'

Note you may need to install the strace package for this to work.

Hope this helps!
Donald

[math_priyanka]

Hello Donald

I’m assuming you are using the bash shell, in which case I expect the output to be /bin/bash

Yes it is /bin/bash

The output of the command
echo exit | strace bash -li |& grep ‘^open’

pc@pc-HP-Pavilion-Laptop-14-dv1xxx:~/Documents/research/data$ echo exit | strace bash -li |& grep '^open'
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/glibc-hwcaps/x86-64-v4/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/glibc-hwcaps/x86-64-v3/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/glibc-hwcaps/x86-64-v2/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/tls/haswell/avx512_1/x86_64/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/tls/haswell/avx512_1/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/tls/haswell/x86_64/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/tls/haswell/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/tls/avx512_1/x86_64/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/tls/avx512_1/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/tls/x86_64/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/tls/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/haswell/avx512_1/x86_64/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/haswell/avx512_1/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/haswell/x86_64/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/haswell/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/avx512_1/x86_64/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/avx512_1/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/x86_64/libreadline.so.8", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/libreadline.so.8", O_RDONLY|O_CLOEXEC) = 3
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/glibc-hwcaps/x86-64-v4/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/glibc-hwcaps/x86-64-v3/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/glibc-hwcaps/x86-64-v2/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/tls/haswell/avx512_1/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/tls/haswell/avx512_1/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/tls/haswell/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/tls/haswell/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/tls/avx512_1/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/tls/avx512_1/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/tls/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/tls/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/haswell/avx512_1/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/haswell/avx512_1/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/haswell/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/haswell/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/avx512_1/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/avx512_1/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/yQt5.14.2/5.14.2/gcc_64/lib/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "glibc-hwcaps/x86-64-v4/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "glibc-hwcaps/x86-64-v3/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "glibc-hwcaps/x86-64-v2/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/haswell/avx512_1/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/haswell/avx512_1/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/haswell/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/haswell/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/avx512_1/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/avx512_1/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "haswell/avx512_1/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "haswell/avx512_1/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "haswell/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "haswell/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "avx512_1/x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "avx512_1/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "x86_64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
openat(AT_FDCWD, "/lib/x86_64-linux-gnu/libdl.so.2", O_RDONLY|O_CLOEXEC) = 3
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "glibc-hwcaps/x86-64-v4/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "glibc-hwcaps/x86-64-v3/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "glibc-hwcaps/x86-64-v2/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/haswell/avx512_1/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/haswell/avx512_1/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/haswell/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/haswell/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/avx512_1/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/avx512_1/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "tls/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "haswell/avx512_1/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "haswell/avx512_1/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "haswell/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "haswell/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "avx512_1/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "avx512_1/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/lib/x86_64-linux-gnu/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./glibc-hwcaps/x86-64-v4/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./glibc-hwcaps/x86-64-v3/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./glibc-hwcaps/x86-64-v2/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./tls/haswell/avx512_1/x86_64/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./tls/haswell/avx512_1/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./tls/haswell/x86_64/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./tls/haswell/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./tls/avx512_1/x86_64/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./tls/avx512_1/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./tls/x86_64/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./tls/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./haswell/avx512_1/x86_64/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./haswell/avx512_1/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./haswell/x86_64/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./haswell/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./avx512_1/x86_64/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./avx512_1/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./x86_64/libtinfo.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/bin/../lib/./libtinfo.so.6", O_RDONLY|O_CLOEXEC) = 3
openat(AT_FDCWD, "/dev/tty", O_RDWR|O_NONBLOCK) = 3
openat(AT_FDCWD, "/usr/lib/locale/locale-archive", O_RDONLY|O_CLOEXEC) = 3
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/nsswitch.conf", O_RDONLY|O_CLOEXEC) = 3
openat(AT_FDCWD, "/etc/passwd", O_RDONLY|O_CLOEXEC) = 3
openat(AT_FDCWD, "/dev/tty", O_RDWR|O_NONBLOCK) = 3
openat(AT_FDCWD, "/home/pc/fsl/share/terminfo/x/xterm-256color", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/profile", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/bash.bashrc", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/profile.d/", O_RDONLY|O_NONBLOCK|O_CLOEXEC|O_DIRECTORY) = 3
openat(AT_FDCWD, "/etc/profile.d/01-locale-fix.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/profile.d/apps-bin-path.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/profile.d/bash_completion.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/usr/share/bash-completion/bash_completion", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/init.d/", O_RDONLY|O_NONBLOCK|O_CLOEXEC|O_DIRECTORY) = 3
openat(AT_FDCWD, "/etc/bash_completion.d/", O_RDONLY|O_NONBLOCK|O_CLOEXEC|O_DIRECTORY) = 3
openat(AT_FDCWD, "/etc/bash_completion.d/apport_completion", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/bash_completion.d/git-prompt", O_RDONLY) = 3
openat(AT_FDCWD, "/usr/lib/git-core/git-sh-prompt", O_RDONLY) = 3
openat(AT_FDCWD, "/dev/null", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
openat(AT_FDCWD, "/etc/profile.d/cedilla-portuguese.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/profile.d/gawk.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/profile.d/gnome-session_gnomerc.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/profile.d/im-config_wayland.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/X11/Xsession.d/70im-config_launch", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/profile.d/vte-2.91.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/profile.d/xdg_dirs_desktop_session.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/.bash_profile", O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/.bash_login", O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/.profile", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/.bashrc", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/.bash_history", O_RDONLY) = 3
openat(AT_FDCWD, "/usr/share/bash-completion/bash_completion", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/init.d/", O_RDONLY|O_NONBLOCK|O_CLOEXEC|O_DIRECTORY) = 3
openat(AT_FDCWD, "/etc/bash_completion.d/", O_RDONLY|O_NONBLOCK|O_CLOEXEC|O_DIRECTORY) = 3
openat(AT_FDCWD, "/etc/bash_completion.d/apport_completion", O_RDONLY) = 3
openat(AT_FDCWD, "/etc/bash_completion.d/git-prompt", O_RDONLY) = 3
openat(AT_FDCWD, "/usr/lib/git-core/git-sh-prompt", O_RDONLY) = 3
openat(AT_FDCWD, "/dev/null", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
openat(AT_FDCWD, "/home/pc/freesurfer/SetUpFreeSurfer.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/freesurfer/FreeSurferEnv.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/fsl/etc/fslconf/fsl.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/fsl/etc/fslconf/fsl.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/fsl/etc/fslconf/fsl.sh", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/.bash_history", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/.bash_history", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/.inputrc", O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/etc/inputrc", O_RDONLY) = 3
openat(AT_FDCWD, "/usr/share/locale/locale.alias", O_RDONLY|O_CLOEXEC) = 3
openat(AT_FDCWD, "/home/pc/fsl/share/locale/en_IN/LC_MESSAGES/bash.mo", O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/fsl/share/locale/en/LC_MESSAGES/bash.mo", O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale-langpack/en_IN/LC_MESSAGES/bash.mo", O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale-langpack/en/LC_MESSAGES/bash.mo", O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/pc/.bash_logout", O_RDONLY) = 3
openat(AT_FDCWD, "/home/pc/.bash_history", O_WRONLY|O_APPEND) = 3

The output of

pc@pc-HP-Pavilion-Laptop-14-dv1xxx:~/Documents/research/$ grep PATH ~/.bashrc ~/.profile ~/.bash_aliases ~/.login ~/.bash_login ~/.bash_profile /etc/profile /etc/bash.bashrc /etc/environment /etc/profile.d/*
/home/pc/.bashrc:export LD_LIBRARY_PATH=/opt/yQt5.14.2/5.14.2/gcc_64/lib:$LD_LIBRARY_PATH
/home/pc/.bashrc:# MRtrix3 PATH automatically generated by set_path script - do NOT modify:
/home/pc/.bashrc:export PATH="/home/pc/mrtrix3/bin:$PATH"
/home/pc/.bashrc:export PATH=/home/pc/ANTs/bin:$PATH
/home/pc/.bashrc:#export PATH=/home/pc/anaconda3/bin:$PATH
/home/pc/.bashrc:#PATH=${FSLDIR}/bin:${PATH}
/home/pc/.bashrc:#export FSLDIR PATH
/home/pc/.profile:# set PATH so it includes user's private bin if it exists
/home/pc/.profile:PATH="$HOME/bin:$PATH"
/home/pc/.profile:# set PATH so it includes user's private bin if it exists
/home/pc/.profile:PATH="$HOME/.local/bin:$PATH"
/home/pc/.profile:#PATH=${FSLDIR}/share/fsl/bin:${PATH}
/home/pc/.profile:export FSLDIR PATH
grep: /home/pc/.bash_aliases: No such file or directory
grep: /home/pc/.login: No such file or directory
grep: /home/pc/.bash_login: No such file or directory
grep: /home/pc/.bash_profile: No such file or directory
/etc/environment:PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
/etc/profile.d/apps-bin-path.sh:# Expand $PATH to include the directory where snappy applications go.
/etc/profile.d/apps-bin-path.sh:if [ -n "${PATH##*${snap_bin_path}}" ] && [ -n "${PATH##*${snap_bin_path}:*}" ]; then
/etc/profile.d/apps-bin-path.sh:    export PATH="$PATH:${snap_bin_path}"
grep: /etc/profile.d/debuginfod.csh: Permission denied
grep: /etc/profile.d/debuginfod.sh: Permission denied
/etc/profile.d/gawk.csh:alias gawkpath_default 'unsetenv AWKPATH; setenv AWKPATH `gawk -v x=AWKPATH "BEGIN {print ENVIRON[x]}"`'
/etc/profile.d/gawk.csh:alias gawkpath_prepend 'if (! $?AWKPATH) setenv AWKPATH ""; if ($AWKPATH == "") then; unsetenv AWKPATH; setenv AWKPATH `gawk -v x=AWKPATH "BEGIN {print ENVIRON[x]}"`; endif; setenv AWKPATH "\!*"":$AWKPATH"'
/etc/profile.d/gawk.csh:alias gawkpath_append 'if (! $?AWKPATH) setenv AWKPATH ""; if ($AWKPATH == "") then; unsetenv AWKPATH; setenv AWKPATH `gawk -v x=AWKPATH "BEGIN {print ENVIRON[x]}"`; endif; setenv AWKPATH "$AWKPATH"":\!*"'
/etc/profile.d/gawk.csh:alias gawklibpath_default 'unsetenv AWKLIBPATH; setenv AWKLIBPATH `gawk -v x=AWKLIBPATH "BEGIN {print ENVIRON[x]}"`'
/etc/profile.d/gawk.csh:alias gawklibpath_prepend 'if (! $?AWKLIBPATH) setenv AWKLIBPATH ""; if ($AWKLIBPATH == "") then; unsetenv AWKLIBPATH; setenv AWKLIBPATH `gawk -v x=AWKLIBPATH "BEGIN {print ENVIRON[x]}"`; endif; setenv AWKLIBPATH "\!*"":$AWKLIBPATH"'
/etc/profile.d/gawk.csh:alias gawklibpath_append 'if (! $?AWKLIBPATH) setenv AWKLIBPATH ""; if ($AWKLIBPATH == "") then; unsetenv AWKLIBPATH; setenv AWKLIBPATH `gawk -v x=AWKLIBPATH "BEGIN {print ENVIRON[x]}"`; endif; setenv AWKLIBPATH "$AWKLIBPATH"":\!*"'
/etc/profile.d/gawk.sh:	unset AWKPATH
/etc/profile.d/gawk.sh:	export AWKPATH=`gawk 'BEGIN {print ENVIRON["AWKPATH"]}'`
/etc/profile.d/gawk.sh:	[ -z "$AWKPATH" ] && AWKPATH=`gawk 'BEGIN {print ENVIRON["AWKPATH"]}'`
/etc/profile.d/gawk.sh:	export AWKPATH="$*:$AWKPATH"
/etc/profile.d/gawk.sh:	[ -z "$AWKPATH" ] && AWKPATH=`gawk 'BEGIN {print ENVIRON["AWKPATH"]}'`
/etc/profile.d/gawk.sh:	export AWKPATH="$AWKPATH:$*"
/etc/profile.d/gawk.sh:	unset AWKLIBPATH
/etc/profile.d/gawk.sh:	export AWKLIBPATH=`gawk 'BEGIN {print ENVIRON["AWKLIBPATH"]}'`
/etc/profile.d/gawk.sh:	[ -z "$AWKLIBPATH" ] && \
/etc/profile.d/gawk.sh:		AWKLIBPATH=`gawk 'BEGIN {print ENVIRON["AWKLIBPATH"]}'`
/etc/profile.d/gawk.sh:	export AWKLIBPATH="$*:$AWKLIBPATH"
/etc/profile.d/gawk.sh:	[ -z "$AWKLIBPATH" ] && \
/etc/profile.d/gawk.sh:		AWKLIBPATH=`gawk 'BEGIN {print ENVIRON["AWKLIBPATH"]}'`
/etc/profile.d/gawk.sh:	export AWKLIBPATH="$AWKLIBPATH:$*"

Now I can manually remove the PATH of /home/pc/fsl/bin (or ~/fsl/bin ).

[jdtournier]

OK, it seems when launching the bash shell from the terminal causes it to load loads of libraries from the FSL-supplied miniconda environment – not great… But at least is allows us to look at the files involved. From the listing, the relevant startup files that a new bash shell looks at are:

/etc/profile
/etc/bash.bashrc
/etc/profile.d/01-locale-fix.sh
/etc/profile.d/apps-bin-path.sh
/etc/profile.d/bash_completion.sh
/etc/profile.d/vte-2.91.sh
/home/pc/.bash_profile [not found]
/home/pc/.bash_login [not found]
/home/pc/.profile
/home/pc/.bashrc

This is good, since these are all included in the list I provided for the text search (the grep command) – so the settings must have been placed somewhere in there.

Looking at the output of the next command, I can see that FSLDIR and the PATH are being set in both ~/.bashrc and ~/.profile – but it looks like you’ve commented out the bit that used to explicitly add FSLDIR to the PATH from the ~/.bashrc (the one in the ~/.profile is also commented out, but that added ${FSLDIR}/share/fsl/bin to the PATH; not necessary if you’re running the fslconf script, but shouldn’t be a problem either way).

From what you’ve shown, I think this should work properly. But it may be that you need to log out and back in again – restarting the terminal may not be enough. The reason is that the settings in ~/.profile may have been applied to your whole desktop session when it started up, and these will then be inherited by any apps launched within that session, including your terminal…

So long story short: try logging out and in again, see if that’s enough to fix the issue.

All the best,
Donald

[math_priyanka]

Thanks. I think the FSL PATH problem is solved.

pc@pc-HP-Pavilion-Laptop-14-dv1xxx:~$ $PATH
bash: /home/pc/fsl/share/fsl/bin:/bin:/home/pc/ANTs/bin:/home/pc/mrtrix3/bin:/home/pc/freesurfer/bin:/home/pc/freesurfer/fsfast/bin:/home/pc/freesurfer/tktools:/home/pc/freesurfer/mni/bin:/home/pc/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin: No such file or directory

but ./configure error for MRTrix3 persists

pc@pc-HP-Pavilion-Laptop-14-dv1xxx:~/MRtrix3Tissue$ ./configure 

MRtrix3Tissue build type requested: release version

MRtrix3Tissue is a fork of the MRtrix3 project

Detecting OS: linux
Looking for compiler [clang++]: Ubuntu clang version 14.0.0-1ubuntu1.1
Checking for C++11 compliance: ok
Checking shared library generation: ok
Detecting pointer size: 64 bit
Detecting byte order: little-endian
Checking for variable-length array support: ok
Checking for non-POD variable-length array support: ok
Checking for ::max_align_t: 16 bytes
Checking for std::max_align_t: 16 bytes
Checking for Eigen3 library: 3.4.0
Checking for zlib compression library: 1.2.11
Checking for "JSON for Modern C++" requirements: ok
Checking for TIFF library: LIBTIFF, Version 4.3.0
Checking for PNG library: Header: 1.6.37; library: 1.6.37
Checking for FFTW library: fftw-3.3.8-sse2-avx
Checking for Qt moc: moc (version 5.14.2)
Checking for Qt qmake: qmake (version 5.14.2)
Checking for Qt rcc: rcc (version 5.14.2)
Checking for Qt: 5.14.2

writing configuration to file './config': ok

[jdtournier]

That’s good, but what error? The configure shows it completed without error, it’s ready to run the ./build. Have you tried building yet?

[math_priyanka]

Yes. I tried ./build many times.

pc@pc-HP-Pavilion-Laptop-14-dv1xxx:~/MRtrix3Tissue$ ./build
(  1/506) [CC] tmp/src/exec_version.o
(  2/506) [CC] tmp/cmd/label2mesh.o
(  3/506) [CC] tmp/src/surface/scalar.o
(  4/506) [CC] tmp/core/image_io/fetch_store.o
(  5/506) [CC] tmp/core/file/nifti1_utils.o
(  6/506) [CC] tmp/core/formats/xds.o
(  7/506) [CC] tmp/core/formats/mri.o
(  8/506) [CC] tmp/core/dwi/gradient.o
(  9/506) [CC] tmp/core/file/dicom/patient.o

ERROR: (  7/506) [CC] tmp/core/formats/mri.o

clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /home/pc/fsl/include -DMRTRIX_PNG_SUPPORT -idirafter /home/pc/fsl/include/libpng16 -idirafter /home/pc/fsl/include -DEIGEN_FFTW_DEFAULT -Wall -O3 -DNDEBUG -Isrc -I./core -Icmd -idirafter /home/pc/fsl/include/eigen3 -DEIGEN_DONT_PARALLELIZE core/formats/mri.cpp -o tmp/core/formats/mri.o

failed with output

In file included from core/formats/mri.cpp:17:
In file included from ./core/file/config.h:21:
./core/types.h:326:9: error: redefinition of 'Vector3' as different kind of symbol
  using Vector3 = Matrix<MR::default_type, 3, 1>;
        ^
/home/pc/fsl/include/eigen3/Eigen/src/Core/Matrix.h:541:1: note: previous definition is here
EIGEN_MAKE_TYPEDEFS(3, 3)
^
/home/pc/fsl/include/eigen3/Eigen/src/Core/Matrix.h:523:67: note: expanded from macro 'EIGEN_MAKE_TYPEDEFS'
template <typename Type>                                          \
                                                                  ^
In file included from core/formats/mri.cpp:17:
In file included from ./core/file/config.h:21:
./core/types.h:327:9: error: redefinition of 'Vector4' as different kind of symbol
  using Vector4 = Matrix<MR::default_type, 4, 1>;
        ^
/home/pc/fsl/include/eigen3/Eigen/src/Core/Matrix.h:542:1: note: previous definition is here
EIGEN_MAKE_TYPEDEFS(4, 4)
^
/home/pc/fsl/include/eigen3/Eigen/src/Core/Matrix.h:523:67: note: expanded from macro 'EIGEN_MAKE_TYPEDEFS'
template <typename Type>                                          \
                                                                  ^
In file included from core/formats/mri.cpp:22:
In file included from ./core/formats/list.h:20:
In file included from ./core/header.h:30:
./core/image_helpers.h:427:20: error: use of alias template 'Eigen::Vector3' requires template arguments
      const Eigen::Vector3 vs1 (in1.spacing(0), in1.spacing(1), in1.spacing(2));
                   ^
/home/pc/fsl/include/eigen3/Eigen/src/Core/Matrix.h:541:1: note: template is declared here
EIGEN_MAKE_TYPEDEFS(3, 3)
^~~~~~~~~~~~~~~~~~~~~~~~~
/home/pc/fsl/include/eigen3/Eigen/src/Core/Matrix.h:523:67: note: expanded from macro 'EIGEN_MAKE_TYPEDEFS'
template <typename Type>                                          \
~~~~~~~~~~~~~~~~~~~~~~~~                                          ^
In file included from core/formats/mri.cpp:22:
In file included from ./core/formats/list.h:20:
In file included from ./core/header.h:30:
./core/image_helpers.h:428:20: error: use of alias template 'Eigen::Vector3' requires template arguments
      const Eigen::Vector3 vs2 (in2.spacing(0), in2.spacing(1), in2.spacing(2));
                   ^
/home/pc/fsl/include/eigen3/Eigen/src/Core/Matrix.h:541:1: note: template is declared here
EIGEN_MAKE_TYPEDEFS(3, 3)
^~~~~~~~~~~~~~~~~~~~~~~~~
/home/pc/fsl/include/eigen3/Eigen/src/Core/Matrix.h:523:67: note: expanded from macro 'EIGEN_MAKE_TYPEDEFS'
template <typename Type>                                          \
~~~~~~~~~~~~~~~~~~~~~~~~

........................................
........................................

This is what I am getting after ./configure.
I thought many be some issues with the versions of prerequisites. But all of them are satisfied.
Is some other path conflicting with the installation? Is the version of Eigen is the problem?

[jdtournier]

OK, yes there is indeed a problem when using Eigen 3.4 with an older version of MRtrix – such as MRtrix3Tissue.

On top of that, you seem to be using the version of Eigen supplied with FSL – not the system-supplied version, which is what I would have expected…

Can you post the contents of your config and configure.log files here? There may be clues in there as to what’s going on…

[math_priyanka]

I have changed the Eigen version in FSL and MRTrix3Tissue has been installed. Thank you Donald for your help.

[jdtournier]

That’s good to hear, glad it worked out.

However, I would urge you to restore the Eigen version in FSL to avoid any unexpected surprises when using FSL. I personally doubt this will cause any trouble, but as a general rule, the reason the FSL team have decided to include this whole miniconda environment with their install is (I expect) to ensure their software uses the exact versions of everything they rely on. If users start changing the packages in that environment, there’s no guarantee FSL will keep working correctly.

The better way to work outside of FSL (e.g. when installing MRtrix) is to make sure their miniconda environment is not accessible directly – which is what most of this discussion has been about, and why their installer states:

@jdtournier

# If this is an official (fslinstaller-installed) FSL
# installation, wrappers to FSL executables will have
# been created in $FSLDIR/share/fsl/bin/ We add this to
# the $PATH, rather than adding $FSLDIR/bin/ to the
# path, to avoid clobbering the user's environment with
# other executalbes that have been installed into
# $FSLDIR/bin/ (e.g.  python).

Given everything we did so far to make sure that folder was not in the PATH, I was surprised to see it using the Eigen version from the FSL install (the /home/pc/fsl/include/eigen3/Eigen folder). I wasn’t expecting that, and I suspect there may still be issues somewhere, which may affect MRtrix or other things. On that basis, I would still like to see the contents of your config and configure.log files so we can figure out what happened and provide better advice the next time a user has a problem of this nature. Would you be happy to post them here?

Thanks and all the best,
Donald

[math_priyanka]

Yes sure. Even when the installation was going on, some warning are apprearing. I dont know whether they have any connection with FSL path.
Here are the contents of config file

#!/usr/bin/python
#
# autogenerated by MRtrix3Tissue configure script
#
# configure output:
# 
# MRtrix3Tissue build type requested: release version
# 
# MRtrix3Tissue is a fork of the MRtrix3 project
# 
# Detecting OS: linux
# Looking for compiler [clang++]: Ubuntu clang version 14.0.0-1ubuntu1.1
# Checking for C++11 compliance: ok
# Checking shared library generation: ok
# Detecting pointer size: 64 bit
# Detecting byte order: little-endian
# Checking for variable-length array support: ok
# Checking for non-POD variable-length array support: ok
# Checking for ::max_align_t: 16 bytes
# Checking for std::max_align_t: 16 bytes
# Checking for Eigen3 library: 3.3.7
# Checking for zlib compression library: 1.2.11
# Checking for "JSON for Modern C++" requirements: ok
# Checking for TIFF library: not found - TIFF support disabled
# Checking for PNG library: Header: 1.6.37; library: 1.6.37
# Checking for FFTW library: fftw-3.3.8-sse2-avx
# Checking for Qt moc: moc (version 5.15.8)
# Checking for Qt qmake: qmake (version 5.15.8)
# Checking for Qt rcc: rcc (version 5.15.8)
# Checking for Qt: 5.15.8

PATH = r'/home/pc/fsl/share/fsl/bin:/home/pc/fsl/bin:/home/pc/ANTs/bin:/home/pc/mrtrix3/bin:/home/pc/freesurfer/bin:/home/pc/freesurfer/fsfast/bin:/home/pc/freesurfer/tktools:/home/pc/fsl/bin:/home/pc/fsl/share/fsl/bin:/home/pc/freesurfer/mni/bin:/home/pc/fsl/share/fsl/bin:/home/pc/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin'
obj_suffix = '.o'
exe_suffix = ''
lib_prefix = 'lib'
lib_suffix = '.so'
cpp = [ 'clang++', '-c', 'CFLAGS', 'SRC', '-o', 'OBJECT' ]
cpp_flags = [ '-std=c++11', '-DMRTRIX_BUILD_TYPE="release version"', '-pthread', '-fPIC', '-DMRTRIX_WORD64', '-idirafter', '/home/pc/fsl/include', '-DMRTRIX_PNG_SUPPORT', '-idirafter', '/home/pc/fsl/include/libpng16', '-idirafter', '/home/pc/fsl/include', '-DEIGEN_FFTW_DEFAULT', '-Wall', '-O3', '-DNDEBUG' ]
ld = [ 'clang++', 'OBJECTS', 'LDFLAGS', '-o', 'EXECUTABLE' ]
ld_flags = [ '-Wl,--sort-common,--as-needed', '-pthread', '-L/home/pc/fsl/lib', '-lz', '-L/home/pc/fsl/lib', '-lpng16', '-lfftw3' ]
runpath = '-Wl,-rpath,$ORIGIN/'
ld_enabled = True
ld_lib = [ 'clang++', 'OBJECTS', 'LDLIB_FLAGS', '-o', 'LIB' ]
ld_lib_flags = [ '-shared', '-Wl,--sort-common,--as-needed', '-pthread', '-L/home/pc/fsl/lib', '-lz', '-L/home/pc/fsl/lib', '-lpng16', '-lfftw3' ]
eigen_cflags = [ '-idirafter', '/home/pc/fsl/include/eigen3', '-DEIGEN_DONT_PARALLELIZE' ]
moc = 'moc'
rcc = 'rcc'
qt_cflags = [ '-pipe', '-std=gnu++11', '-Wall', '-Wextra', '-D_REENTRANT', '-fPIC', '-DQT_NO_DEBUG', '-DQT_OPENGL_LIB', '-DQT_SVG_LIB', '-DQT_WIDGETS_LIB', '-DQT_GUI_LIB', '-DQT_CORE_LIB', '-idirafter', '/home/pc/fsl/include/qt', '-idirafter', '/home/pc/fsl/include/qt/QtOpenGL', '-idirafter', '/home/pc/fsl/include/qt/QtSvg', '-idirafter', '/home/pc/fsl/include/qt/QtWidgets', '-idirafter', '/home/pc/fsl/include/qt/QtGui', '-idirafter', '/home/pc/fsl/include/qt/QtCore', '-idirafter', '/home/pc/fsl/include', '-idirafter', '/usr/include/libdrm', '-idirafter', '$(CONDA_BUILD_SYSROOT)/usr/include', '-idirafter', '/home/pc/fsl/mkspecs/linux-g++' ]
qt_ldflags = [ '-Wl,-O1', '-Wl,-rpath,/home/pc/fsl/lib', '/home/pc/fsl/lib/libQt5OpenGL.so', '/home/pc/fsl/lib/libQt5Svg.so', '/home/pc/fsl/lib/libQt5Widgets.so', '/home/pc/fsl/lib/libQt5Gui.so', '/home/pc/fsl/lib/libQt5Core.so', '-L$(CONDA_BUILD_SYSROOT)/usr/lib64', '-lGL', '-lpthread' ]
nogui = False

Content of configure.log file

REPORT: 
MRtrix3Tissue build type requested: release version

MRtrix3Tissue is a fork of the MRtrix3 project

REPORT: Detecting OS: linux

REPORT: Looking for compiler [clang++]:
EXEC <<
CMD: clang++ --version
EXIT: 0
STDOUT:
Ubuntu clang version 14.0.0-1ubuntu1.1
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
>>


REPORT: Ubuntu clang version 14.0.0-1ubuntu1.1

REPORT: Checking for C++11 compliance:

COMPILE /tmp/tmpphghoamq.cpp:
---

#include <cstddef>
struct Base {
    Base (int);
};
struct Derived : Base {
    using Base::Base;
};

int main() {
  Derived D (int); // check for contructor inheritance
  return 0;
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC /tmp/tmpphghoamq.cpp -o /tmp/tmpphghoamq.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpphghoamq.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
>>


REPORT: ok

REPORT: Checking shared library generation:
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC /tmp/tmpv82slgux.cpp -o /tmp/tmpv82slgux.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpv82slgux.o -shared -Wl,--sort-common,--as-needed -pthread -o libtest.so
EXIT: 0
>>


REPORT: ok

REPORT: Detecting pointer size:

COMPILE /tmp/tmpmyq3h5sw.cpp:
---

#include <iostream>
int main() {
  std::cout << sizeof(void*);
  return (0);
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC /tmp/tmpmyq3h5sw.cpp -o /tmp/tmpmyq3h5sw.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpmyq3h5sw.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
8
>>


REPORT: 64 bit

REPORT: Detecting byte order:

REPORT: little-endian

REPORT: Checking for variable-length array support:

COMPILE /tmp/tmpiwof2g3v.cpp:
---

int main(int argc, char* argv[]) {
  int x[argc];
  return 0;
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmpiwof2g3v.cpp -o /tmp/tmpiwof2g3v.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpiwof2g3v.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
>>


REPORT: ok

REPORT: Checking for non-POD variable-length array support:

COMPILE /tmp/tmpltb7v4h2.cpp:
---

#include <string>

class X {
  int x;
  double y;
  std::string s;
};

int main(int argc, char* argv[]) {
  X x[argc];
  return 0;
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmpltb7v4h2.cpp -o /tmp/tmpltb7v4h2.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpltb7v4h2.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
>>


REPORT: ok

REPORT: Checking for ::max_align_t:

COMPILE /tmp/tmp0q4hmmyo.cpp:
---

#include <iostream>
#include <cstddef>
using ::max_align_t;
int main() {
  std::cout << alignof (max_align_t) << " bytes\n";
  return 0;
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmp0q4hmmyo.cpp -o /tmp/tmp0q4hmmyo.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmp0q4hmmyo.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
16 bytes
>>


REPORT: 16 bytes

REPORT: Checking for std::max_align_t:

COMPILE /tmp/tmpyqek6wlo.cpp:
---

#include <iostream>
#include <cstddef>
using std::max_align_t;
int main() {
  std::cout << alignof (max_align_t) << " bytes\n";
  return 0;
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmpyqek6wlo.cpp -o /tmp/tmpyqek6wlo.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpyqek6wlo.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
16 bytes
>>


REPORT: 16 bytes
EXEC <<
CMD: pkg-config --cflags eigen3
EXIT: 0
STDOUT:
-I/home/pc/fsl/include/eigen3
>>


REPORT: Checking for Eigen3 library:

COMPILE /tmp/tmp7qr8xp0x.cpp:
---

#include <cstddef>
#include <Eigen/Core>
#include <iostream>

int main (int argc, char* argv[]) {
  std::cout << EIGEN_WORLD_VERSION << "." << EIGEN_MAJOR_VERSION << "." << EIGEN_MINOR_VERSION << "\n";
  return 0;
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /home/pc/fsl/include/eigen3 /tmp/tmp7qr8xp0x.cpp -o /tmp/tmp7qr8xp0x.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmp7qr8xp0x.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
3.3.7
>>


REPORT: 3.3.7
EXEC <<
CMD: pkg-config --cflags zlib
EXIT: 0
STDOUT:
-I/home/pc/fsl/include
>>

EXEC <<
CMD: pkg-config --libs zlib
EXIT: 0
STDOUT:
-L/home/pc/fsl/lib -lz
>>


REPORT: Checking for zlib compression library:

COMPILE /tmp/tmpu1anzeqy.cpp:
---

#include <iostream>
#include <zlib.h>

int main() {
  std::cout << zlibVersion();
  return (0);
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /home/pc/fsl/include /tmp/tmpu1anzeqy.cpp -o /tmp/tmpu1anzeqy.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpu1anzeqy.o -Wl,--sort-common,--as-needed -pthread -L/home/pc/fsl/lib -lz -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
1.2.11
>>


REPORT: 1.2.11

REPORT: Checking for "JSON for Modern C++" requirements:

COMPILE /tmp/tmpun8pwn2f.cpp:
---

#include "file/json.h"
int main (int argc, char* argv[])
{
  nlohmann::json json;
  json["key"] = "value";
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /home/pc/fsl/include -I/home/pc/MRtrix3Tissue/core /tmp/tmpun8pwn2f.cpp -o /tmp/tmpun8pwn2f.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpun8pwn2f.o -Wl,--sort-common,--as-needed -pthread -L/home/pc/fsl/lib -lz -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
>>


REPORT: ok
EXEC <<
CMD: pkg-config --cflags libtiff-4
EXIT: 0
STDOUT:
-I/home/pc/fsl/include -I/home/pc/fsl/include/webp -I/home/pc/fsl/include
>>

EXEC <<
CMD: pkg-config --libs libtiff-4
EXIT: 0
STDOUT:
-L/home/pc/fsl/lib -ltiff
>>


REPORT: Checking for TIFF library:

COMPILE /tmp/tmpps7awzv9.cpp:
---

#include <iostream>
#include <tiffio.h>

int main() {
  std::cout << TIFFGetVersion();
  return (0);
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /home/pc/fsl/include -idirafter /home/pc/fsl/include -idirafter /home/pc/fsl/include/webp -idirafter /home/pc/fsl/include /tmp/tmpps7awzv9.cpp -o /tmp/tmpps7awzv9.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpps7awzv9.o -Wl,--sort-common,--as-needed -pthread -L/home/pc/fsl/lib -lz -L/home/pc/fsl/lib -ltiff -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 127
STDERR:
./a.out: error while loading shared libraries: libtiff.so.6: cannot open shared object file: No such file or directory
>>


REPORT: not found - TIFF support disabled
EXEC <<
CMD: pkg-config --cflags libpng
EXIT: 0
STDOUT:
-I/home/pc/fsl/include/libpng16 -I/home/pc/fsl/include
>>

EXEC <<
CMD: pkg-config --libs libpng
EXIT: 0
STDOUT:
-L/home/pc/fsl/lib -lpng16
>>


REPORT: Checking for PNG library:

COMPILE /tmp/tmpxma2i3p4.cpp:
---

#include <iostream>
#include <png.h>

int main() {
  std::cout << "Header: " << PNG_LIBPNG_VER_STRING << "; library: " << png_libpng_ver;
  return (0);
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /home/pc/fsl/include -idirafter /home/pc/fsl/include/libpng16 -idirafter /home/pc/fsl/include /tmp/tmpxma2i3p4.cpp -o /tmp/tmpxma2i3p4.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpxma2i3p4.o -Wl,--sort-common,--as-needed -pthread -L/home/pc/fsl/lib -lz -L/home/pc/fsl/lib -lpng16 -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
Header: 1.6.37; library: 1.6.37
>>


REPORT: Header: 1.6.37; library: 1.6.37
EXEC <<
CMD: pkg-config --cflags fftw3
EXIT: 1
STDERR:
Package fftw3 was not found in the pkg-config search path.
Perhaps you should add the directory containing `fftw3.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fftw3' found
>>

error running "pkg-config --cflags fftw3"

EXEC <<
CMD: pkg-config --libs fftw3
EXIT: 1
STDERR:
Package fftw3 was not found in the pkg-config search path.
Perhaps you should add the directory containing `fftw3.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fftw3' found
>>

error running "pkg-config --libs fftw3"


REPORT: Checking for FFTW library:

COMPILE /tmp/tmp8at3hfn2.cpp:
---

#include <iostream>
#include <fftw3.h>

int main() {
  std::cout << fftw_version << "\n";
  return (0);
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /home/pc/fsl/include -DMRTRIX_PNG_SUPPORT -idirafter /home/pc/fsl/include/libpng16 -idirafter /home/pc/fsl/include /tmp/tmp8at3hfn2.cpp -o /tmp/tmp8at3hfn2.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmp8at3hfn2.o -Wl,--sort-common,--as-needed -pthread -L/home/pc/fsl/lib -lz -L/home/pc/fsl/lib -lpng16 -lfftw3 -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
fftw-3.3.8-sse2-avx
>>


REPORT: fftw-3.3.8-sse2-avx

REPORT: Checking for Qt moc:
EXEC <<
CMD: moc -v
EXIT: 0
STDOUT:
moc 5.15.8
>>


REPORT: moc (version 5.15.8)

REPORT: Checking for Qt qmake:
EXEC <<
CMD: qmake -v
EXIT: 0
STDOUT:
QMake version 3.1
Using Qt version 5.15.8 in /home/pc/fsl/lib
>>


REPORT: qmake (version 5.15.8)

REPORT: Checking for Qt rcc:
EXEC <<
CMD: rcc -v
EXIT: 0
STDOUT:
rcc 5.15.8
>>


REPORT: rcc (version 5.15.8)

REPORT: Checking for Qt:

source file "qt.h":
---
#include <QObject>

class Foo: public QObject {
  Q_OBJECT;
  public:
    Foo();
    ~Foo();
  public slots:
    void setValue(int value);
  signals:
    void valueChanged (int newValue);
  private:
    int value_;
};
---

source file "qt.cpp":
---
#include <iostream>
#include "qt.h"

Foo::Foo() : value_ (42) { connect (this, SIGNAL(valueChanged(int)), this, SLOT(setValue(int))); }

Foo::~Foo() { std::cout << qVersion() << "\n"; }

void Foo::setValue (int value) { value_ = value; }

int main() { Foo f; }
---

project file "qt.pro":
---
CONFIG += c++11
QT += core gui opengl svg
HEADERS += qt.h
SOURCES += qt.cpp
---
EXEC <<
CMD: qmake
EXIT: 0
STDOUT:
Info: creating stash file /tmp/tmpafki11db/.qmake.stash
>>

EXEC <<
CMD: moc qt.h -o qt_moc.cpp
EXIT: 0
>>

EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /home/pc/fsl/include -DMRTRIX_PNG_SUPPORT -idirafter /home/pc/fsl/include/libpng16 -idirafter /home/pc/fsl/include -DEIGEN_FFTW_DEFAULT -pipe -std=gnu++11 -Wall -Wextra -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -idirafter /home/pc/fsl/include/qt -idirafter /home/pc/fsl/include/qt/QtOpenGL -idirafter /home/pc/fsl/include/qt/QtSvg -idirafter /home/pc/fsl/include/qt/QtWidgets -idirafter /home/pc/fsl/include/qt/QtGui -idirafter /home/pc/fsl/include/qt/QtCore -idirafter /home/pc/fsl/include -idirafter /usr/include/libdrm -idirafter $(CONDA_BUILD_SYSROOT)/usr/include -idirafter /home/pc/fsl/mkspecs/linux-g++ qt.cpp -o qt.o
EXIT: 0
>>

EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /home/pc/fsl/include -DMRTRIX_PNG_SUPPORT -idirafter /home/pc/fsl/include/libpng16 -idirafter /home/pc/fsl/include -DEIGEN_FFTW_DEFAULT -pipe -std=gnu++11 -Wall -Wextra -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -idirafter /home/pc/fsl/include/qt -idirafter /home/pc/fsl/include/qt/QtOpenGL -idirafter /home/pc/fsl/include/qt/QtSvg -idirafter /home/pc/fsl/include/qt/QtWidgets -idirafter /home/pc/fsl/include/qt/QtGui -idirafter /home/pc/fsl/include/qt/QtCore -idirafter /home/pc/fsl/include -idirafter /usr/include/libdrm -idirafter $(CONDA_BUILD_SYSROOT)/usr/include -idirafter /home/pc/fsl/mkspecs/linux-g++ qt_moc.cpp -o qt_moc.o
EXIT: 0
>>

EXEC <<
CMD: clang++ -Wl,--sort-common,--as-needed -pthread -L/home/pc/fsl/lib -lz -L/home/pc/fsl/lib -lpng16 -lfftw3 qt_moc.o qt.o -o qt -Wl,-O1 -Wl,-rpath,/home/pc/fsl/lib /home/pc/fsl/lib/libQt5OpenGL.so /home/pc/fsl/lib/libQt5Svg.so /home/pc/fsl/lib/libQt5Widgets.so /home/pc/fsl/lib/libQt5Gui.so /home/pc/fsl/lib/libQt5Core.so -L$(CONDA_BUILD_SYSROOT)/usr/lib64 -lGL -lpthread
EXIT: 0
>>

EXEC <<
CMD: /tmp/tmpafki11db/qt
EXIT: 0
STDOUT:
5.15.8
>>


REPORT: 5.15.8

I can share the build.log file also.

[jdtournier]

OK, thank you, much appreciated. I can see that /home/pc/fsl/bin is still in the PATH, which explains why it’s using packages from FSL rather than your system ones. It looks like we still haven’t worked out exactly where your PATH is being set…

But no matter – if it works for you at the moment, I don’t think there’s anything to worry about at this stage. Though I wouldn’t be surprised if you find some unexpected behaviour down the line. For instance, I expect you’ll be using the python version from the FSL environment by default (you can check with which python), and that may cause issues with other python commands & packages – depending on exactly how they’re set up, etc. Something to watch out for, I guess…

All the best,
Donald.

[AlexandraBonthrone]

Hi All,

I was having this same issue and on my system (20.04 Ubuntu). I tracked it down to the Freesurfer environment setting script (freesurfer/7.4.1/FreeSurferEnv.sh) which was adding $FSLDIR/bin to the path. I commented out the freesurfer setup from my shell setup (mine was in /etc/profile) and then MRtrix built with no issues.

All the best,
Alex