HI - I guess that means that you didn't copy renderhighres into the right
place correctly - could you run the following and email me the output:
ls -lrt $FSLDIR/bin
Cheers, Steve.
On Fri, 29 Jul 2005, Stella de Bode wrote:
> That was it, sorry, i did not formulate it right. Did it, Stephen.
> Now, when i try running <renderhighres>, it simply answers <command not
> found>. Sorry
> S
>
> On Jul 29, 2005, at 7:35 AM, Stephen Smith wrote:
>
> >
> > Ah - I think I've finally understood what Stella's asking - sorry it's
> > taken so long! The problem is that renderhighres isn't happy about an
> > image called "highres" not existing - and didn't give a useful error
> > message to this effect....
> >
> > In any case, the GUI and script were a bit limited as they were - so
> > we've
> > just re-written the GUI and the script to both be more useful and solve
> > your issue - the output is now created in an "hr" subdirectory in the
> > FEAT
> > output directory. Don't forget that FEAT and this new GUI thinks that
> > your
> > structural image is the "standard" image.
> >
> > So - save the two attached files, and:
> > chmod a+x renderhighres
> > cp renderhighres ${FSLDIR}/bin
> > cp renderhighres.tcl ${FSLDIR}/tcl
> >
> > Hopefully that should work!
> >
> >
> >
> > On Fri, 29 Jul 2005, Mark Jenkinson wrote:
> >
> >> Hi Stella,
> >>
> >> I didn't realise you were using the command line version of
> >> renderhighres. In that case you want to use both the -tal
> >> and -keep options. If you use the GUI, then select the
> >> button that I suggested before.
> >>
> >> All the best,
> >> Mark
> >>
> >>
> >> On 28 Jul 2005, at 22:45, Stella de Bode wrote:
> >>
> >>> I do use -keep, Stephen. <Renderhighres> will not run at all for me
> >>> after i do Feat with registration on the subject's HR only (in
> >>> "standard" space), no Initial/Main images. I wonder what i can do to
> >>> renderhighres. Thanks
> >>> S
> >>>
> >>>
> >>> On Jul 28, 2005, at 5:16 PM, Stephen Smith wrote:
> >>>
> >>>> Hi - I'm not quite sure what you're asking here - is it just that
> >>>> you
> >>>> need
> >>>> the -keep option so that the 3D files don't get cleaned up after the
> >>>> GIF
> >>>> images are made?
> >>>>
> >>>> Cheers.
> >>>>
> >>>> On Thu, 28 Jul 2005, Stella de Bode wrote:
> >>>>
> >>>>> Sorry. I am still stuck with <renderhighres> function. After I
> >>>>> run
> >>>>> FEAT with all suggested changes "Do rendering in Tal. splace" and
> >>>>> no
> >>>>> search and the subject's HR instead of standard (and decent
> >>>>> registration as a result), I still cannot run renderhighres
> >>>>> file.feat
> >>>>> z-min z-max. I am lacking hr_thresh_zstat files, i think this is
> >>>>> the
> >>>>> problem, but i am not sure how to fix it. I think, somebody during
> >>>>> class suggested that i should concurrently run registration on
> >>>>> example_func to produce this hr file, but I am not sure how to do
> >>>>> it.
> >>>>> Sorry, thank you!
> >>>>> On Jul 28, 2005, at 11:52 AM, Christian Beckmann wrote:
> >>>>>
> >>>>>> sorry, it's the bottom right corner of the main gui - I mixed up
> >>>>>> left
> >>>>>> and right, guess I've been driving in england for too long ;)
> >>>>>> christian
> >>>>>>
> >>>>>>
> >>>>>> On 28 Jul 2005, at 16:29, Stella de Bode wrote:
> >>>>>>
> >>>>>>> Thank you, Mark. This button you are talking about, "rendering
> >>>>>>> in
> >>>>>>> Tal. space>, where is it? I usually enter <renderhighres> as a
> >>>>>>> command line and i don't see it under FSL bar. Sorry, it's,
> >>>>>>> probably, obvious.
> >>>>>>> Thank you very much. Stella
> >>>>>>> On Jul 27, 2005, at 9:20 AM, Mark Jenkinson wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>> Hi Stella,
> >>>>>>>>
> >>>>>>>> Glad you enjoyed the course.
> >>>>>>>>
> >>>>>>>> I'm also glad that the registrations are working with the no
> >>>>>>>> search
> >>>>>>>> option.
> >>>>>>>> I assume you are now using the individual's structural image as
> >>>>>>>> the
> >>>>>>>> "standard" image in the feat registration setup. If this is the
> >>>>>>>> case then
> >>>>>>>> you also need to ask renderhighres to render into the "standard"
> >>>>>>>> space,
> >>>>>>>> rather than into highres space. You can do this by selecting
> >>>>>>>> the
> >>>>>>>> "Do rendering in Talairach space instead of original high res
> >>>>>>>> space"
> >>>>>>>> button
> >>>>>>>> in the GUI. Rest assured that in your case it won't do the
> >>>>>>>> rendering in
> >>>>>>>> actual Talairach space, as it uses whatever image you've put as
> >>>>>>>> the
> >>>>>>>> "standard"
> >>>>>>>> for its definition of "Talairach" space (which in your case will
> >>>>>>>> be
> >>>>>>>> the
> >>>>>>>> individual's structural).
> >>>>>>>>
> >>>>>>>> I hope that fixes the problem.
> >>>>>>>> Let us know if this doesn't work or you need help with another
> >>>>>>>> aspect of
> >>>>>>>> the registration work.
> >>>>>>>>
> >>>>>>>> All the best,
> >>>>>>>> Mark
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> stella de Bode wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> Thanks for an excellent class! I would like to follow up with
> >>>>>>>>> Mark
> >>>>>>>>> re performing registration when a lesion is half a brain.
> >>>>>>>>> When i
> >>>>>>>>> follow Mark's suggestion and register it with "No Search" using
> >>>>>>>>> the
> >>>>>>>>> patient;s high-res instead of a standard, the registration
> >>>>>>>>> works
> >>>>>>>>> smoothly. But I cannot run <renderhighres> then, i need to
> >>>>>>>>> somehow
> >>>>>>>>> input a functional scan as initial. I am not sure how to
> >>>>>>>>> reach
> >>>>>>>>> the stage when both registration is correct and rendehighres is
> >>>>>>>>> possible. Thank you so much! Stella
> >>>>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Christian F. Beckmann
> >>>>>> Oxford University Centre for Functional
> >>>>>> Magnetic Resonance Imaging of the Brain,
> >>>>>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> >>>>>> Email: [log in to unmask] -
> >>>>>> http://www.fmrib.ox.ac.uk/~beckmann/
> >>>>>> Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
> >>>>>
> >>>>
> >>>> --
> >>>> 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
> >>
> >
> > --
> > 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
> >
> >
> >
> >
> >
> >
> > <renderhighres.tcl><renderhighres>
>
--
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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