Hi Steve,
I'm afraid to say I don't get any dtifit output in the subj1 directory. I
only get dtifit output if I use the terminal. With the GUI, I
instantaneously get a pop-up window with the output referred to below, then
a 'Done!' window, and nothing else. I have this same sort of problem with
the Probtrack GUI too.
Nad
On Thu, 27 Oct 2005 18:48:05 +0100, Stephen Smith <[log in to unmask]>
wrote:
>Hi - when I start Cygwin, run Fdt_gui, select dtifit, and select the
>fdt_subj1 input directory and press OK, all runs ok, though it does finish
>with an "error...slices processed" message - but the dtifit output is
>correctly created in the fdt_subj1 directory.
>
>Hope this helps? Cheers, Steve.
>
>
>On Wed, 26 Oct 2005, Nachiket Nadkarni wrote:
>
>> 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
>>
>
>--
> Stephen M. Smith DPhil
> Associate Director, FMRIB and Analysis Research Coordinator
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>=========================================================================
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