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Atlases and fslview

FSL's fslview allows the use of atlases in conjunction with your data.

You may run into problems with fslview being unable to find the atlas files. This problem is related to the default atlas location chosen when fslview is launched, which is determined by the values of the current set of environment variables. It is best to use module load fsl prior to launching any FSL program, this will ensure that the environment is set up for use on our grid environment.

If you follow the procedure above and fslview still cannot locate the atlas files, it is likely that the wrong location was written to the configuration file. To fix, you may set the locations for the atlas files using the Preferences dialog for fslview, found at File -> Preferences... -> FSL. The image below illustrates this dialog along with paths correct for the grid version of FSL 5.0.8:

Preferences (FSL) Dialog

Alternatively, you may simply delete the configuration file. It is stored in your home directory under the hidden .config directory:

~/.config/fmrib.ox.ac.uk/fslview.conf

This will cause fslview to rewrite it the next time it is launched. In this case, it will use paths derived from the current environment settings, so it is best to use the first procedure of this article and set your environment with module load fsl</version> where </version> is an optional fsl version.

Note that removing this file will reset other custom settings for fslview, including the geometry (location and size) of the initial window.