Hi all,
Because of a local lack of Linux computers, I am looking into installing
FSL on CygWin. For reasons of portability (eg being able to make a copy
of a cygwin image and put it on another computer) I wanted to keep
everything as small as possible.
After first installing FSL with its own libs (ie having `freeware' in
the build script), which went fine, I also installed FSL using the libs
already in cygwin (gnuplot, tcl/tk, etc).
In both cases, after a little fidgeting, everything installed OK: the
build script ends with a message that everything has been successfully
installed.
I type fsl, and sure enough the interface comes up. but pressing the
buttons for the FSL tools has no effect! Nothing happens.
I looked at fsl.tcl to see what was happening, and when I removed the
"&" from the command line used for the BET option, I got this error
message:
> Error: You need to source an FSL setup file - either fsl.sh or
> fsl.csh in $FSLDIR/etc/conf! child process exited abnormally
But this should not be necessary. When I type
> env|grep FSL
I get:
> FSLMULTIFILEQUIT=TRUE
> FSLGNUPLOT=/usr/local/fsl/bin/gnuplot
> FSLMACHTYPE=i686-pc-cygwin-gcc3.4.4
> FSLTCLSH=/usr/local/fsl/bin/tclsh
> FSLMACHINELIST=
> FSLREMOTECALL=
> FSLCONFDIR=/usr/local/fsl/config
> FSLWISH=/usr/local/fsl/bin/wish
> FSLBROWSER=/cygdrive/c/Program Files/Firefox/firefox.exe
> FSLDISPLAY=/usr/local/fsl/bin/display
> FSLCONVERT=/usr/local/fsl/bin/convert
> FSLDIR=/usr/local/fsl
> FSLLOCKDIR=
> FSLOUTPUTTYPE=NIFTI
showing that both the system-wide fsl.sh and my own copy (that sets
FSLOUTPUTTYPE to NIFTI) have been read.
I don't know enough about tcl to know why in Bet_gui, these environment
variables are not present. Has anyone ever had similar problems in cygwin?
Note that this happens in both FSL with own libraries (freeware) and
with the cygwin-supplied libraries.
Thanks for your help,
Alle Meije Wink
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