andrewsilberfeld
commented
1 year ago 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`
Hello,
The inverse transform function is missing the lines to automatically count the number of processes when processes term is None:
also, when those lines are added back to the Elastix.py script and clearmap2 is restarted, Elastix throws an error because it references a file set in Christoph's directory:
The first error can be fixed by adding the "if processes is None: ..." lines to "inverse_transform()" and restarting clearmap. Not sure how to fix this second error right now.