Computed tomography
From UCL HEP PBT Wiki
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== Introduction == | == Introduction == | ||
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| + | This tutorial will based on the DICOM GEANT4 example originally developed by Louis Archambault, Luc Beaulieu and Vincent Hubert-Tremblay. In this example a DICOM file is converted to a simple ASCII file, where the Hounsfield numbers are converted to materials and densities so that it can be used by GEANT4. It also creates a GEANT4 geometry based on the DICOM file information using the '''G4PhantomParameterisation'''. | ||
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== Setting up the environment == | == Setting up the environment == | ||
| - | == How to get the code == | + | |
| - | == How to run the code == | + | ; Connect to HEP cluster and create folder DICOMFolder in your area |
| - | == How to analyze data == | + | |
| + | <pre style="color: #800000; background-color: #dcdcdc"> | ||
| + | ssh -X username@plus1.hep.ucl.ac.uk | ||
| + | |||
| + | password: type your password here | ||
| + | |||
| + | cd /home/username/ | ||
| + | |||
| + | mkdir DICOMFolder | ||
| + | |||
| + | cd DICOMFolder | ||
| + | </pre> | ||
| + | |||
| + | ; Setup your environment | ||
| + | |||
| + | <pre style="color: #800000; background-color: #dcdcdc"> | ||
| + | source /unix/pbt/software/dev/bin/pbt-dev.sh | ||
| + | </pre> | ||
| + | |||
| + | == <span style="color:#000080"> How to get the code </span> == | ||
| + | |||
| + | ; Copy the code to your working directory and rename it | ||
| + | |||
| + | <pre style="color: #800000; background-color: #dcdcdc"> | ||
| + | cp -r /unix/pbt/tutorials/basic/DICOM . | ||
| + | |||
| + | mv DICOM DICOM_source | ||
| + | </pre> | ||
| + | |||
| + | == <span style="color:#000080"> How to run the code </span> == | ||
| + | |||
| + | ; Inside /home/username/DICOMFolder/ create a directory | ||
| + | |||
| + | <pre style="color: #800000; background-color: #dcdcdc"> | ||
| + | mkdir DICOM_build | ||
| + | </pre> | ||
| + | |||
| + | ; To compile the code enter this directory and run cmake and make | ||
| + | |||
| + | <pre style="color: #800000; background-color: #dcdcdc"> | ||
| + | cd DICOM_build | ||
| + | |||
| + | cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DICOMFolder/DICOM_source | ||
| + | |||
| + | make | ||
| + | </pre> | ||
| + | |||
| + | ; Run macro run.mac. | ||
| + | |||
| + | <pre style="color: #800000; background-color: #dcdcdc"> | ||
| + | ./DICOM run.mac | ||
| + | </pre> | ||
| + | |||
| + | == <span style="color:#000080"> How to analyze data </span> == | ||
