FAQ
Q: Error information "error in GenerateDendritePopulation" pop-up after automatic tracing. No neuron is traced.
A: This error information means that GTree cannot reorganize the traced neurites into completed neurons with tree structure. This often happens when tracing high density neuronal images. We guess that tree structure of the target neuron is broken in high density neuronal image. We will address it later. If needed we can also provide GTree which does not reorganise neuron tree structure and only output traced neurites.
A: According to https://github.com/GTreeSoftware/GTree/wiki/System-Requirement, The VC++ 2017 x64 redistribution should be installed first. It can be downloaded from https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads. We also provide the corresponding VC++ runtime installer "vcredist_msvc2017_x64.exe" in GTree windows archive file above 1.0.4 version (i.e. https://github.com/GTreeSoftware/GTree/releases/tag/1.0.4.3). If the error still occurs, install VC++ 2008-2019 together. This package is very important for Windows programs such as 3D game, Autocad, 3Ds-Max, et al.
A: 1. please update the Windows system and install the latest official patch. From VC++ 2015, the old version Windows systems are be not supported. For example, SP1 patch should be installed on Windows server 2012 for installing VC++2015.
- If the Windows system is not old, please use DISM.exe to repair the system library and reboot the computer. Then install VC++ 2017 again.
A:
- The reason is that GPU is weak or GPU driver software is broken. GTree requires discrete graphics card (GPU) to visualize the 3D volume image. Please Re-install the corresponding GPU driver. For Linux on the virtual machine, the OpenGL version supported is limited, thus it is not suggested to run GTree on the virtual machine. To check whether the GPU driver is installed well on Linux, please run the command "sudo apt-get install mesa-utils" to install glxinfo tool. Then run command "glxinfo | grep OpenGL" to get the GPU driver information. Example information of well-installed GPU driver is as follows:
OpenGL version string: 4.6.0 NVIDIA 440.100
OpenGL shading language version string: 4.60 NVIDIA
- Check GTree directory and ensure whether plugin directories "platforms" and "xcbglintegrations" exist. GTree for Windows does not require "xcbglintegrations" plugin directory.
Q: Cannot run GTree on Linux, qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
A: It means that plugin directories "platforms" and "xcbglintegrations" do not exist. Please (1) use the new version of GTree above 1.0.4 version (i.e. https://github.com/GTreeSoftware/GTree/releases/tag/1.0.4.3). Or (2) download and install Qt 5 library from http://download.qt.io/ .
A: The error message means that the user's Linux version is low and GTree is compiled on higher version Linux. GLIBC is the basic C runtime library of Linux and we do not recommend upgrading glibc beyond the official support. Please upgrade the Linux or compile the GTree project on low version Linux.
A: In most cases the reasons are: 1. Reference to error libraries 2. Lost libraries 3. The GLIBC required by GTree is not found, or the glibc version is low, which means the Linux version is low.
A: In most cases, user install both Visual Studio 2017 and 2019. The Conan will download the 3rd libraries for Visual Studio 2019 in default. If user introduces the libraries acquired from Conan and compiles GTree using Visual Studio 2017, this error occurs. The solution is that compiling GTree using Visual Studio 2019, or uninstalling Visual Studio 2019 and re-installing 3rd libraries for Visual Studio 2017 using Conan.
Q: Compile GTree on Linux and error ocurs : ".so: file format not recognized; treating as linker script"; Or "/usr/bin/ld: cannot find -lvtkXXXX"
A: This problem occurs when user uses the downloaded prebuilt binary libraries and: 1. User decompresses the library zip file on Windows and copy the decompressed library files to Linux. The soft link of Linux library files will be broken on Windows. 2. User extracts the libraries zip file into the disk formatted by Windows. The Windows disk formats such as NTFS, exFAT32, do not support Linux library files and soft link files. 3. User right-click the library zip file and decompress the file. Run "ls -al" command and user will find that the soft link ".so*-->[Real file]" is broken and the terminal just shows ".so*". As we know, there is a bug in the old version Unzip software. The soft link of Linux library files will be broken. We recommend the user running the command "sudo unzip [packagename]" in terminal to decompress the prebuilt binary library zip file and keep the soft link well. More information please refer to https://github.com/binance-exchange/binacpp/issues/15
A: In big data mode (TDat/Mostd, HDF5), Soma location, tracing and manual editing operation should be performed under image-level 1, which refers to the original images. Image-level number N, refers to 2^(N-1) downsampled images. Low-resolution images (image-level 2~N, level N refer to the lowest resolution images. The maximum level can be seen in mostd directory) are only used to locate the region of interest.
Q: Windows GTree will suspend after starting long time work. User must press the "enter" button in CMD window of GTree to resume GTree.
A: In old version Windows, the program with CMD will be suspended automatically if there is no interactive operation for a long time. And if users select the words in CMD window, the program will also be suspended. Users need to press any key in CMD window to resume the program. There are 2 solutions: 1. Update the Windows system. 2. Turn off the Quick Edit mode and insert mode of CMD window.
A: Please make sure that Qt 5 has been installed and Qt VS Tools in Visual Studio has been installed and well configured. Please right-click on the "Solution GTree_VS2017" and click "Change solution's Qt version" to reset the Qt 5 version. It is a bug of Qt VS Tools.
A: The Windows SDK kit of Visual Studio is not installed or configured correctly. Please click Project-->Properties--->General-->Windows SDK Versions and set the installed SDK version.
A: Please see https://github.com/GTreeSoftware/GTree/wiki/GUI-Difference-between-Windows-Linux . The GUI interfaces of different versions of Linux and Windows are different. GTree introduces Qt 5, the cross-platform GUI framework. The Qt 5 GUI on different systems is determined by the corresponding system GUI component.
- Introduction
- User Manual
- Demo Movie
- Testing Data
- System Requirement
- GUI Difference of Win/Linux
- Tree Structure
- Soma Localization
- Neuron Tracing
- Manual Revision
- Error Checking
- Big-Data
- Batch Tracing
- Shape Reconstruction
- SWC Reorganization
- Shortcut Key
- TODO