HI,

I have downloaded cygwin, and installed fsl into c:/cygwin/usr/local using fsl_installer.sh and fsl-4.1.9_centos5_32.tar.gz downloaded from the fsl website. I have edited the setpaths.bat files in both c:/yale/bioimage3_base and c:/yale/bioimagesuite30 with

@set FSLDIR=/usr/local/fsl
@set CYGWINDIR=c:/cygwin
@set WFSLDIR=%CYGWINDIR%/%FSLDIR%
@set FSLOUTPUTTYPE=ANALYZE

I can't get bioimagesuite to see FSL in the path.  I don't know whether the above should be added at a certain location in the setpaths.bat file, I put it in the end.  I don't know if it even matters (I have no experience in computer programming). 

I also noticed that the binary files for fsl are in c:/cygwin/usr/local/fsl/bin and changed the first line to reflect this in both setpaths.bat

@set FSLDIR=/usr/local/fsl/bin

but also to no avail.  I still get FSL not found.

Can you help with this?

Thanks!

Chang Ho