Jiansong,
FSL is included with Freesurfer, but it looks like our package may not include everything that you use.
The solution for you is to setup the FSL_DIR environment variable prior to the Freesurfer setup, like this:
setenv FSL_DIR /usr/local/fsl source $FREESURFER_HOME/SetUpFreeSurfer.csh
This will cause freesurfer to setup your local FSL instead of the one included with freesurfer.
Freesurfer uses the 'flirt' utility in its recon-all stream, but as long as your fsl package is relatively recent (3.2 or newer), the recon-all should be ok.
Nick
Dear Friends:
My fsl was installed in the directory /usr/local/fsl.
I can use fsl before download freesurfer, but I cannot open fsl any more after installed FreeSurfer. Any suggestions?
Thanks
Jiansong
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