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
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