Configuring analysis machine

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Under Construction

Installing Pyctf

Download the pyctf folder 

 git clone $USER@$GITSERVER:pyctf
 cd $PYCTF_FOLDER_PATH
 make 
 make symlinks 
 #This may error out if you have the mkl library installed >> you can create another conda environment conda creat -n compile python=3.7 nomkl numpy >> conda activate compile >> make >> make symlinks

Add the pyctf path to your pythonpath variable 

 PYTHONPATH=$PYTHONPATH:$PYCTF_FOLDER_PATH

If you are using an Anaconda python manager

  • Create a file pyctf.pth
 echo $PYCTF_FOLDER_PATH > pyctf.pth
  • Add at pyctf_pth file to your Anaconda folder
 For example /home/User/miniconda3/envs/ENV_NAME/lib/python3.7/site-packages/pyctf.pth

Installing SAMsrc

 #Install gsl
 #Fedora
 sudo dnf install nifticlib-devel
 sudo dnf install gifticlib-devel
 sudo dnf install motif motif-devel
 sudo dnf install fftw fftw-devel
 sudo dnf install libpng12.x86_64
 sudo dnf install -y tcsh libXp op  ## Not sure of the op
 sudo dnf install gsl, gsl-devel    ## If errors when running SAM software, you may need to link the library

Linking thd_atr

 #Afni related functions
 ln -s $SAM/lib/thd_atr $PYCTF_dir/thd_atr


Installing Afni

https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/index.html

  1. If issue with libgsl.so.0:: sudo ln -s /usr/lib64/libgsl.so.23 /usr/lib64/libgsl.so.0 << replace the 23 with whichever version of the library you have


Installing CTF software

To view and process the data using the native ctf software, the packages have been incorporated into a singularity container
Install singularity on your computer 

 #Fedora Linux
 sudo dnf install singularity

 #Redhat/Centos Linux
 sudo yum install singularity

 #Ubuntu/Debian Linux 
 sudo apt-get install singularity-container

Download the current CTF singularity container and components

  • ctf.sif
  • wrap
  • mkwrappers
 cd $Directory_With_CTF_Container
 mkwrappers  #This will install the container in /usr/local/ctf/bin and the links to all of the functions in /usr/local/ctf/bin

Environmental Variables that may need to be modified

  • CTF_DATADIR
  • CTF_MRIDIR
  • CTF_WORKDIR

Enabling jupyter lab widgets

 dnf install nodejs
 conda install -c conda-forge ipywidgets
 jupyter nbextension enable --py widgetsnbextension
 jupyter labextension install @jupyter-widgets/jupyterlab-manager

https://ipywidgets.readthedocs.io/en/latest/user_install.html

Enabling GUI

 download pygobject (gtk3) from anaconda https://anaconda.org/conda-forge/pygobject
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