a simple C++ graph analysis library
License: MIT License
A simple, crossplatform C++ graph analysis library for brain functional connectivity.
financially sponsored by Brain Innovation B.V.
Eigen C++
Boost BGL
Download and extract the source packages of Boost and Eigen at ../third-party/boost and ../third-party/eigen3 respectively.
I try to compile this project in order to calculate some graph metrics and get the correlation matrix and adjacency matrix of a resting-state fMRI (4D). I am not sure how to implement though the NIfTI reading, and what input is getting used by brainnets? Is it the raw 4D matrix from NIfTI? E.g. in my case that is a (45,51,45,167) matrix.
Is it possible to attach an example of a use case of reading an input fMRI and calculating some metrics (also pinpointing where the correlation matrix/adjacency matrix are saved?)
Have you tried a multithreading approach as well?
Thank you for your time.
Trying to compile on macOS Big Sur 11.6.5 (20G527) with Qt 6.2 and Boost v1.78.0 and Eigen v3.4.0 I am getting the following compilation error:
cd brainnets/ && ( test -e Makefile || /usr/local/bin/qmake -o Makefile /Users/wizofe/Projects/neuro/brainnets/brainnets/brainnets.pro ) && /Library/Developer/CommandLineTools/usr/bin/make -f Makefile
cd brainnets/ && ( test -e Makefile || /usr/local/bin/qmake -o Makefile /Users/wizofe/Projects/neuro/brainnets/brainnets/brainnets.pro ) && /Library/Developer/CommandLineTools/usr/bin/make -f Makefile
/Library/Developer/CommandLineTools/usr/bin/clang++ -c -pipe -stdlib=libc++ -std=c++11 -O2 -std=gnu++1z -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -mmacosx-version-min=11 -Wall -Wextra -fPIC -DBRAINNETS_LIBRARY -DQT_NO_DEBUG -I../../brainnets -I. -I../../../third-party -I../../../third-party/boost -I../../../third-party/eigen3 -I/usr/local/share/qt/mkspecs/macx-clang -o ../../builds/release/brainnets-tmp/networks_mst.o ../networks_mst.cpp
In file included from ../networks_mst.cpp:10:
In file included from ../../../third-party/boost/boost/graph/prim_minimum_spanning_tree.hpp:15:
../../../third-party/boost/boost/graph/dijkstra_shortest_paths.hpp:100:62: warning: unused parameter 'u' [-Wunused-parameter]
template < class Edge, class Graph > void tree_edge(Edge u, Graph& g) {}
^
../../../third-party/boost/boost/graph/dijkstra_shortest_paths.hpp:100:72: warning: unused parameter 'g' [-Wunused-parameter]
template < class Edge, class Graph > void tree_edge(Edge u, Graph& g) {}
^
../../../third-party/boost/boost/graph/dijkstra_shortest_paths.hpp:253:40: warning: unused parameter 'g' [-Wunused-parameter]
static type build(const Graph& g, const IndexMap& index,
^
../../../third-party/boost/boost/graph/dijkstra_shortest_paths.hpp:254:43: warning: unused parameter 'array_holder' [-Wunused-parameter]
boost::scoped_array< Value >& array_holder)
^
../../../third-party/boost/boost/graph/dijkstra_shortest_paths.hpp:302:40: warning: unused parameter 'g' [-Wunused-parameter]
static type build(const Graph& g, const IndexMap& index)
^
clang: error: unable to execute command: Segmentation fault: 11
clang: error: clang frontend command failed due to signal (use -v to see invocation)
Apple clang version 13.0.0 (clang-1300.0.29.30)
Target: x86_64-apple-darwin20.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
clang: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang: note: diagnostic msg: /var/folders/kt/4jcwh7_x3d3bnyblfzk4945w0000gn/T/networks_mst-12f2b5.cpp
clang: note: diagnostic msg: /var/folders/kt/4jcwh7_x3d3bnyblfzk4945w0000gn/T/networks_mst-12f2b5.sh
clang: note: diagnostic msg: Crash backtrace is located in
clang: note: diagnostic msg: /Users/wizofe/Library/Logs/DiagnosticReports/clang_<YYYY-MM-DD-HHMMSS>_<hostname>.crash
clang: note: diagnostic msg: (choose the .crash file that corresponds to your crash)
clang: note: diagnostic msg:
********************
make[2]: *** [../../builds/release/brainnets-tmp/networks_mst.o] Error 254
make[1]: *** [sub-brainnets-make_first] Error 2
make: *** [sub-brainnets-make_first] Error 2
Any idea why?
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