Thanks for the quick response...
1) Both my functionals and structurals contain 12 slices in the same
location and orientation. So, I am thinking it should be a pretty basic
overlay of the functionals onto the structurals. The first-level FEAT
report works out just fine. The output contains all 12 of my functional
slices. However, when I try to use the renderhighres function, only 6
slices are contained in the outputted Rendered_hr_thresh_zstat1.gif.
Hopefully, this is enough info. Any suggestions?
2) Thanks...I'll give it a try.
On Friday, December 6, 2002, at 10:22 AM, Stephen Smith wrote:
> Hi.
>
> 1) is it the original functional or the structural that contains 12
> slices
> originally? I'm not quite clear what you are asking - a little more
> details would probably be useful: the FEAT report shows activaiton
> overlaid in lowres (original FMRI resolution) for a first-level
> analysis;
> the registration page shows various views of the registration results;
> if
> you use the Renderhighres function (a separate GUI from FEAT) then the
> resulting images will either be in the space of the highres images or
> standard space.
>
> 2) sure - you can change the orientation using avwswapdim. For example,
> you could do
>
> avwswapdim inputimage x y -z outputimage
> to get the slices in the reverse order, OR
>
> avwswapdim inputimage -x y -z outputimage
> to achieve a rotation about the line from nose to the back of the
> head...
>
> Thanks, Steve.
>
>
> On Fri, 6 Dec 2002, David Krauss wrote:
>
>> 1) In FEAT, when rendering the activation maps onto the high res
>> images, the output only contains 6 slices even though my slice
>> prescriptions contained 12 slices. Are these slices just a random
>> sampling of my slices, are they chosen somehow systematically, or am I
>> just doing something wrong?
>>
>> 2) I have one subject whose brain I need to invert. Are there any good
>> FSL tools to do this, and can I apply the same tool to my functional
>> and hi-res images?
>>
>>
>> David Krauss
>> Graduate Student
>> UCLA Department of Psychology
>> [log in to unmask]
>>
>
> Stephen M. Smith
> Head of Image Analysis, FMRIB
>
> 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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