Installing FSL and FIX on Linux: Legacy R/MATLAB Setup and Modern Python FIX

Installing FSL and FIX on Linux involves two distinct approaches: the legacy R/MATLAB method and the modern Python-based FIX included with recent FSL versions. The article separates these methods for clarity.

FSL, short for FMRIB Software Library, is a suite of tools for MRI analysis. FIX, or FMRIB's ICA-based Xnoiseifier, identifies and removes noise from fMRI data. The article distinguishes between the two installation scenarios: the current Python-based FIX, included with FSL 6.0.7.8 and newer, and the legacy R/MATLAB FIX, no longer supported.

To install FSL on Linux, use the getfsl.sh script, which installs FSL into the user's home directory. After installation, verify the environment using specific commands. For the legacy method, the Python installer was used, though this approach is no longer recommended.

The legacy R/MATLAB FIX installation required downloading a tar.gz archive, extracting its contents, installing specific R packages, and moving the FIX directory to /usr/local. This method depended on certain packages, including MATLAB toolboxes and R versions. Installing this version involved more manual steps and potential system compatibility issues.

For new installations, the Python-based FIX, included with recent FSL versions, is recommended. This method does not require separate R or MATLAB installations. An example command demonstrates using the Python FIX with a pretrained model. However, successful ICA classification and cleaned fMRI results are not guaranteed by this command alone.

In summary, while both installation methods exist, the modern Python-based FIX is the preferred approach for new Linux installations of FSL. The legacy R/MATLAB FIX, although documented, is no longer recommended due to its complexity and potential compatibility issues.