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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer