Hi all,

I successfully installed cygwin, fsl and ran feeds with no errors.

My intention is to use Fdt, so I decided to practise using the data from the 
Fdt lecture from the FSL Course, as I couldn't find instructions for using 
the FEEDS Fdt data.

FSL View worked fine, so I went ahead and used DTIFit. However, the GUI 
produced this when I followed the lecture's instructions and pressed 'Go':


Errors:
dtifit

Usage:
dtifit -k <filename>
dtifit --verbose


Compulsory arguments (You MUST set one
or more of):
-k,--data    dti data file
-o,--out    Output basename
-m,--mask Bet binary mask file
-r,--bvecs b vectors file
-b,--bvals b values file

Optional arguments (You may optionally
specify one or more of):
-V,--verbose switch on
diagnostic messages
-h,--help   display this message
--littlebit   Only process small
area of brain

-z,--zmin min z
-Z,--zmax max z
-y,--ymin min y
-Y,--ymax max y
-x,--xmin min x
-X,--xmax max x


Specifying the files manually made no difference. This looks exactly like 
the output when "dtifit" is typed into the cygwin terminal (i.e.: an output 
of the parameters that can be set). The above output was displayed in a 
separate window that appeared instantaneously and could not be copied or 
pasted from so I had to type the output manually! The window also had an OK 
button at the bottom, and after this was pressed the window disappeared and 
another small window appeared with the word "Done!" plus an OK button which 
got rid of this 'Done!' window when pressed.

Using the instructions in the same lecture for the terminal interface, I 
managed to run dtifit and produce output which could be viewed in FSL View 
with no problems.

Probtrack produced the same sort of result as dtifit. I tried to use the 
terminal interface with probtrack to see whether it worked but the parameter 
settings required were too complex for me to deal with.

In short, my terminal interface works but my gui seems to not do anything 
useful. I can just about use the terminal but don't have much experience 
with it so would appreciate some help if there is no option. I found 
instructions for using dtifit with terminal commands but the probtrack 
parameters look a lot more complex and don't seem to fully tally up with the 
gui parameters for which there is advice.

Thanks for your help

Nachiket Nadkarni