Using FSL with a GridEngine (or similar) computing cluster To bring up a simple GUI which is just a menu of the main individual FSL GUI tools, just type fsl.

Bet), except on macOS, where you need to append _gui because it can't tell the difference between upper and lower case filenames (e.g. bet), with the GUI version capitalised (e.g. In general, command-line programs are lower case (e.g. Once your account is configured for FSL use, you can run the FSL tools from the command line the tools are stored in $FSLDIR/bin and this location will have been added to your terminal's search locations for ease of use. On Linux computers it can also be used to configure FSL for all users on the computer. See our shell setup guide for details on what this script does. The FSL Install script will setup your computer such that you can run the FSL tools from a terminal. Note that this will cause a large amount of data to be downloaded - a fast and reliable internet connection is necessary in order for the installation to complete successfully. Run sudo $FSLDIR/etc/fslconf/fslpython_install.sh -f $FSLDIR to re-install the missing components. If it does, delete it by running sudo rm -r $FSLDIR/fslpython. To fix this, follow these steps (you may be able to omit sudo if you installed FSL into a location other than /usr/local/fsl/):Ĭheck to see if a directory called $FSLDIR/fslpython exists. If, after installing FSL, FSLeyes is missing, or you encounter errors such as imcp: No such file or directory (or similar errors referring to imglob or immv), then this means that the installation did not complete successfully.

Troubleshooting: commands missing after installation Once you have downloaded the installer, fslinstaller.py, you can use it to install FSL on your computer by following these instructions (click on the appropriate link now, as the next steps for installing are described in the linked pages, not in the sections immediately below here):Īfter you have installed FSL for the first time, you can update your version to keep up with new releases by following these instructions to apply upgrades/patches (e.g. We strongly recommend that the FSL software is downloaded and installed using the fslinstaller.py script available from the link below: We also provide source code if you run an OS not directly supported by us.

Running bedpostX on a GPU or GPU clusterįSL is available ready to run for macOS and Linux (Centos or Debian/Ubuntu) - with Windows computers being supported via the Windows Subsystem for Linux (WSL).

Using FSL with a GridEngine (or similar) computing cluster.

Troubleshooting: commands missing after installation.

Mac download file terminal