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andrewsilberfeld avatar andrewsilberfeld commented on August 30, 2024

Pretty sure the the 2nd error "DisplacementMagnitudePenalty(index 3) - This component is not installed!" is due to the initial build of Elastix -- either it lacks that specific file or the file directory is permanently pointed toward a directory on Christoph's machine.

Either way, I decided to install Elastix using CMake on my linux machine and that works well. This can be done by first installing ITK

`module load git/2.35.3 gcc/6.2.0 cmake/3.22.2 #this loads various libraries in my institution's high performance computing cluster.
cd /path/to/my/folder/
mkdir itk
cd itk
git clone https://github.com/InsightSoftwareConsortium/ITK
mkdir build
cd build
cmake ../ITK/ #took 2 min.
make -j4 #took 1.5 hours

#Install Elastix!
module load git/2.35.3 gcc/6.2.0 cmake/3.22.2
cd /path/to/my/folder/
git clone https://github.com/SuperElastix/elastix.git
cd elastix
mkdir build
cd build
cmake .. -DITK_DIR=/path/to/my/folder/itk/build/
make install`

from clearmap2.

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