Hi Tim,
No text appears in the terminal
Nad
On Fri, 28 Oct 2005 11:52:54 +0100, Tim Behrens <[log in to unmask]>
wrote:
>Nad -
>If you start the Fdt GUI from a terminal (type Fdt) and then do your
>dtifit as before, do you get any text appearing in the original terminal.
>If so, could you copy it into an email.
>
>Thanks
>
>T
>
>
>On Fri, 28 Oct 2005, Nachiket Nadkarni wrote:
>
>> 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
>>
>=========================================================================
>>
>
>--
>---------------------------------------------------------------------------
----
>Tim Behrens
>Centre for Functional MRI of the Brain
>The John Radcliffe Hospital
>Headley Way Oxford OX3 9DU
>Oxford University
>Work 01865 222782
>Mobile 07980 884537
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