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BioMedIA / MIRTK

The Medical Image Registration ToolKit (MIRTK), the successor of the IRTK, contains common CMake build configuration files, core libraries, and basic command-line tools. Extension packages are hosted by the MIRTK GitHub group at
https://github.com/MIRTK
Apache License 2.0
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Installation problems #773

Open ghost opened 3 years ago

ghost commented 3 years ago

Hello, I hope you are doing well.

I am having troubles installing MIRTK. I followed your instructions here https://mirtk.github.io/install.html after downloading the MIRTK and submodules (I mostly require DrawEM submodule). I first had errors during the 'make' stage where I had to unzip the DrawEM atlases in Packages/DrawEM/atlases/src myself + additional issues with N4 compilation failing (solved when I disabled ThirdParty/ANTs in CMakeLists.txt). Subsequently, make install runs fine and together with the autocompletion commands the mirtk seems to 'work' at first glance. However, when I try to run the 'mirtk neonatal-segmentation ' I run into <>/mirtk/lib/scripts/preprocess.sh : No such file or directory. Error: neonatal-segmentation command returned non-zero exit status 1.

<>/mirtk/lib/scripts/ indeed does not exist. Do you have any advice how to resolve this issue?

On a related note, I also tried to get the MIRTK with a viewer application with: wget -O mirtk https://bintray.com/schuhschuh/AppImages/download_file?file_path=MIRTK-latest-x86_64-glibc2.14.AppImage

This however leads to a 403 fobidden message. Maybe you have tips on that as well?

Thanks in advance. Best, Andrea

schuhschuh commented 3 years ago

Hi Andrea, if your OS is Linux, try downloading the AppImage using this URL: https://bintray.com/schuhschuh/AppImages/download_file?file_path=MIRTK-2.1-pre2-x86_64-glibc2.14.AppImage

soundray commented 3 years ago

I have a similar issue. Andreas, the AppImage link seems to be dead.

Update: I compiled ANTs in full and separately, then copied N4BiasFieldCorrection to $MIRTK_BINARY_DIR/lib/tools/N4 -- now mirtk neonatal-segmentation seems to be working. Also, it seemed to be necessary to export DRAWEMDIR=$MIRTK_SOURCE_DIR/Packages/DrawEM.