transform-points command : Missing executable!

[ece7048]

Hello,

I build-install the MIRTK in a Linux Ubuntu 16.04 OS . When I am going to use the 'mirtk transform-points' , there is the following ERROR:

Error: Missing executable for command: transform-pointsError: transform-points command returned non-zero exit status 1

Any ideas?

Thank you for your time, Mike

[schuhschuh]

First I would check where the MIRTK files were copied to on your system when you ran "make install". In the output of that command you should see that it copies the binary "transform-points" to the "${CMAKE_INSTALL_PREFIX}/lib/[mirtk/]tools" folder. Next you can check the value of the variable "libexec_dir" defined in "${CMAKE_INSTALL_PREFIX}/lib/python/mirtk/subprocess.py". It should point to aforementioned folder. I suspect that this path may be set incorrect by out CMake scripts used to generate this Python module for your installation. Could you post the paths for your system?

If this doesn't work, note that there's an easy way to install pre-built binaries on any Linux system using the AppImage available on bintray. See https://mirtk.github.io/getstarted.html for more details.

[WangRoss]

I am facing the same problem several days, I nearly cry to a sea. Error: Missing executable for command: transform-pointsError I can not find "transform-points" in /opt/mirtk/lib/tools, though I found its source .cpp file in MIRTK source folder. Then I turned to get help from your Appimage address, but it returned 440. Would you like to inspire me what happend and how to solve it? Great thanks!

[schuhschuh]

Sorry, @WangRoss, have you built MIRTK with option WITH_VTK=ON and MODULE_PointSet=ON?

The transform-points command requires MODULE_Image=ON, MODULE_Transformation=ON, and MODULE_PointSet=ON. (I also recommend WITH_TBB=ON for multi-threading in general; it's off by default).

The AppImage you can download from: https://bintray.com/schuhschuh/AppImages/MIRTK/master#files

[maximedieudonne]

Hi all, hi @schuhschuh, @WangRoss, @ece7048 :) Thanks a lot for this great tool but I have the same problem. I build install the MIRTK in a linux ubuntu 20. When i run a commande like :

mirtk calculate-surface-map example_mesh.gii example_mesh_surface.gii

I get :

Error: Missing executable for command: calculate-surface-map
Error: calculate-surface-map command returned non-zero exit status 1

The same for others commands. My install folder is : /home/maxime/callisto/repo/MIRTK/build/ in my subprocess.py : libexec_dir = os.path.realpath(os.path.join(dir, '../../tools'))

I had in my bashrc : export PATH="/home/maxime/callisto/repo/MIRTK/build/bin:$PATH"

any idea ? thanks a lot :)

[maximedieudonne]

Hi I finally solve my issue : Some dependencies were missing. So I install/compile all the dependency manually and i do some change in makefile to link all my lib to .so file an it finally work

[cherise215]

Hi. I found the solution, which took me several hours as I need to learn the CMake command. So to save others' time and have more time enjoy their life, I just share my solution. It may not be perfect. But it works for me on a Linux machine.

1. Install VTK

following the instructions here add the path to the environment variable.

export VTK_DIR=/path/VTK-Release-version/build

2. Install MIRTK installation guide

• for MIRTK, it is important to compile it and get binary files.

git clone --depth 1 -- https://github.com/BioMedIA/MIRTK.git
MIRTK_SOURCE_DIR="$PWD/MIRTK"
cd $MIRTK_SOURCE_DIR
git submodule update --init
mkdir Build
MIRTK_BINARY_DIR=$MIRTK_SOURCE_DIR/Build
cd $MIRTK_BINARY_DIR

Open path/to/MIRTK/CMake/Config/Settings.cmake,

Add the two lines after line 57 to turn on options with VIK and PointSet for mesh registration:

basis_update_value(MODULE_PointSet ON)
basis_update_value(WITH_VTK ON)

Recompile it with makefile tool, e.g., CMAKE to build binaries from scratch

cmake .. -DVTK_DIR=$path/to/vtk/build$
make -j 8
make install

You make need sudo rights to build, i.e., sudo make install if you build binaries and save under opt/.