Note
Make sure Python version |python_version| is used for installation. Download links can be found here: https://www.python.org/downloads/
Installation as well as opening fRAT for the first time may take a while.
This creates an isolated environment for the fRAT application and will allow you to run it from anywhere.
First install brew:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Then use brew to install pipx:
brew install pipx pipx ensurepath
pipx can then be upgraded with:
brew update && brew upgrade pipx
You will need Python 3.10 on your path. One way to do this is by using the method described below, however this can also be achieved by using miniconda or mamba.
Warning
If using Conda or Anaconda to install Python, the Tkinter version downloaded alongside Python may not have access
to the Freetype library. In this case the GUI will not render text properly, with text appearing as the wrong size
or missing style settings such as bold. If the Run analysis, Run statistics, Run plotting settings on
the General page are bold, then the GUI is rendering properly.
If desired, although not recommended this can be fixed by removing Conda's Tkinter. This causes Python to use the system's Tkinter library:
conda remove --force tk
Install python 3.10:
sudo add-apt-repository ppa:deadsnakes/ppa sudo apt update sudo apt install python3.10
Install necessary packages:
sudo apt install bc python3-pip python3-venv python3.10-distutils python3.10-tk
Install pipx using pip:
python3 -m pip install --user pipx python3 -m pipx ensurepath
pipx can then be upgraded with:
python3 -m pip install --user -U pipx
Note
For WSL2 users, if the example data files are downloaded to windows before being copied over to linux, redundant "zone identifier" files may have been created in the example data folders and you may not have write access to this folder. To change this:
sudo find /home/<WSLUserName>/Documents/fRAT/ -exec chmod a+rwx {} ";"
find /home/<WSLUserName>/Documents/fRAT/ -type f -name "*:Zone.Identifier" -exec rm -rf {} +
pipx install frat-brain --python $(which python3.10)
fRAT can now be ran from the terminal from anywhere by using:
fRAT
fRAT can also be upgraded using:
pipx upgrade frat-brain
The FSL_ neuroimaging software tool is a core component of fRAT and is not able to be downloaded through Python’s Package Index (PyPI), therefore FSL_ (version |fsl_version| or above) should be downloaded and setup separately using FSL's installation instructions.
While optiBET_ is not required for fRAT (link), it is highly recommended that this software tool be used for brain extraction due to the necessity of accurate skull stripping for the fRAT to function optimally and the consistently better brain extraction performance when using optiBET.
1. Create the directory to save the example data folder:
mkdir ~/Documents/fRAT
This allows fRAT to find the example data. This folder will also be used to save configuration profiles in the future.
2. Download the example dataset from here.
3. Extract the folder and place it in the newly created fRAT folder.
4. Click the :guilabel:`General` button in the fRAT section of the GUI and then click the
:guilabel:`Run installation tests` button.
The sample analysis will take roughly 15 minutes on a machine with atleast 4 cores. fRAT will output progress to the
terminal. After the analysis has completed, the output will be compared to those already present in the example_data
folder and will warn if any files are missing. If you want to check the output of the sample analysis, set the
"delete_test_folder" option to "Never".
Note
During the sample analysis, warnings may occur. This is expected and does not indicate that fRAT is not running correctly.