I am installing castor , and I use “ccmake” to generate “makefile”,like this:
CASTOR_CONFIG /home/cdy/castor/castor_v3.1.1/config
CASTOR_CONFIG_DIR /home/cdy/castor/castor_v3.1.1/include/manage
CASToR_64bits ON
CASToR_BUILD_DEVEL OFF
CASToR_BUILD_GATE_UTILITIES ON
CASToR_BUILD_SAMPLE_UTILITIES ON
CASToR_DEBUG OFF
CASToR_MPI OFF
CASToR_OMP ON
CASToR_ROOT ON
CASToR_SIMD ON
CASToR_VERBOSE ON
CMAKE_BUILD_TYPE Release
CMAKE_INSTALL_PREFIX /home/cdy/castor/install
Thank you for your kind help. But when I turn it off like this:
CASTOR_CONFIG /home/cdy/castor/castor_v3.1.1/config
CASTOR_CONFIG_DIR /home/cdy/castor/castor_v3.1.1/include/manage
CASToR_64bits ON
CASToR_BUILD_DEVEL OFF
CASToR_BUILD_GATE_UTILITIES ON
CASToR_BUILD_SAMPLE_UTILITIES ON
CASToR_DEBUG OFF
CASToR_MPI OFF
CASToR_OMP ON
CASToR_ROOT ON
CASToR_SIMD OFF
CASToR_VERBOSE ON
CMAKE_BUILD_TYPE Release
CMAKE_INSTALL_PREFIX /home/cdy/castor/install
Hi,
CASToR requires ROOT for some utilities. Your error comes from a file related to root functions but it is hard to tell it is the issue without more details.
Do you still have an error if you set the ROOT and UTILITIES options to OFF ?
Thank you for your help , I failed installing CASTOR like you say. But I install it with makefile successfully. There is another question ,I want to learn more about reconstruction of GATE PET .
But when I search “https://www.castorproject.org/files/castor/castor_training_tmp/cstr_training_demos.zip”,
it show “The requested page could not be found.” So that ,I can not install the zip.
Is there another way to down load the training-zip?
Hi,
I am not sure where did you find the link but those files were just training data to be used for a short course, and were only planned to be online temporary.
However the section 9 of the documentation covers the utilities, and among them how to use the GATE converters. It should be helpful regarding how to use these tools. Do not hesitate if you have any question though.
I am very grateful for your enthusiastic help. I am a new user both for GATE and CASToR . And now , I just have ".mac " and the output “.root”. I know the steps:
get the .lut file from the .geom file
2.get .cdh/.cdf file from the .lut file
3.use the .cdh/.cdf file to get .img
But I can not understand how to use the “.mac” or “.root” to get my own “.geom”. Is there some examples or teaching video .
To convert your “.mac” to a “.geom”, you need to use the utility castor-GATEMacToGeom. Similarly, to convert GATE output (“.root” files) to CASToR datafiles (“.Cdh” and “.Cdf”), you can use castor-GATERootToCastor.
To use these utilities, you need to compile CASToR with CASToR_BUILD_GATE_UTILITIES=ON.
You will find additional information about these tools in section 9.2 of CASToR documentation.
Then , I used directly the makefile it offered directly like:
export CASTOR_ROOT=1
export CASTOR_GATE_UTILITIES=1
export CASTOR_CONFIG=/home/cdy/castor/castor_v3.1.1/config
But when I used ,it still showed: can not find the CASTOR_CONFIG.I think I’m already going crazy. Could you help me please?
I think this cannot be correct, as GATE utilities rely on ROOT to operate. You need to keep CASToR_ROOT=ON. (Also, I don’t know if it matters, but it should be “CASToR” with lowercase “o”.)
Do you get the error during compilation or after, when using CASToR? Could you copy-paste the exact error message that you are getting?
I am sure that it is the problem with the root. The question below always appears ,when turn CASTOR_ROOT to ON.
like this:
/home/cdy/GATE/root/include/ROOT/RStringView.hxx:32:37: error: ‘experimental’ in namespace ‘std’ does not name a type
using basic_string_view = ::std::experimental::basic_string_view<_CharT,_Traits>;
/home/cdy/GATE/root/include/ROOT/RStringView.hxx:35:12: error: ‘basic_string_view’ does not name a type; did you mean ‘basic_streambuf’?
typedef basic_string_view string_view;
Hi,
Maybe a potential C++ standard mismatch, ROOT being compiled with a given C++ standard while CASToR enforces C++11. You can check C++ standard used to compile ROOT with root-config --features.
If they are different, could you follow the steps from the following thread ?
(use the CMakeLists.txt provided in the discussion, and set CXX_FLAGS to the one used to compile ROOT)
It is possible that the problem comes from Amide (see [1]). Do you have access to another software that can read Interfile image to quickly validate if the problem is on Amide side?
Thank you for your reply. In fact, I did open the file directly in .Raw format. Even when I opened the file using IMAGEJ, the image still looks like this. I’m wondering if there’s an issue with my input file. Are there any relevant examples, such as the output ROOT and MAC files from GATE in PET? I’d like to see what the normal process and results look like.
Could you share pet_it9.{hdr/img}? The (possible) problem about Amide linked previously is about Endianness not being read correctly. Therefore, opening the .img as a raw is one way to make sure IF you use the good Endianness.
Here is my output, https://we.tl/t-iKxWKIWkWr.
It seems like I’m not opening the file correctly. Even when I try opening the examples on the official website, I still encounter the same issue. Is there any tips while open the file?
