Some questions/annotations about lightbox-function

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Some questions/annotations about lightbox-function

andreas_fe
Hello,

I want do display functional MRI data and I had some questions.

I load the structual image as BG and the activation in FG
(Volumens Module). Then I select the range of points I want do display (which
I can see in the histogramm)...

I can select to display about 12 slices at the same time, by selecting the
the view of 6x2 (lightbox)

Question:
-----------

1) how can I choose specify slices... the 1 and 10 and 20.
So every forth slices, one slice should be displayed...

Now I see only a slider? (I think the slider is for "cube" of the structural
images?

2)
as my functional information come from a 64x64x23 "cube", It think it would be
nice to directly display these slices... and not the one I get from the
structural images?
( => I think there must be an interpolation now...)

3)
and it would also be nice to have an export function to png, eps or some other
file format?
for the lightbox-view? (now I have to do a screenshot, and remove the orange
box (on the top left...) by
an image manipulation program. )

4)
it would also be nice if I can specifiy a part of brain to display in the
lightbox, for example the back part of the brain.

5)
(It would be also very nice if every of these steps can be done in a batch
mode or script... are there any plans for such kind of feature?)


Andreas
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Re: Some questions/annotations about lightbox-function

pieper
Administrator
Hi Andreas -

Some feedback mixed in-line below...

On 09/28/2010 12:41 PM, Andreas Fe wrote:

> Hello,
>
> I want do display functional MRI data and I had some questions.
>
> I load the structual image as BG and the activation in FG
> (Volumens Module). Then I select the range of points I want do display (which
> I can see in the histogramm)...
>
> I can select to display about 12 slices at the same time, by selecting the
> the view of 6x2 (lightbox)
>
> Question:
> -----------
>
> 1) how can I choose specify slices... the 1 and 10 and 20.
> So every forth slices, one slice should be displayed...
>
> Now I see only a slider? (I think the slider is for "cube" of the structural
> images?

By default each cell of the lightbox will be one 'slice spacing' appart
- this may be just a mm and all will look similar.  You can set the
spacing mode to 'prescribed' and pick a number like 10mm.

>
> 2)
> as my functional information come from a 64x64x23 "cube", It think it would be
> nice to directly display these slices... and not the one I get from the
> structural images?
> ( =>  I think there must be an interpolation now...)
>

If you pick the spacing to be equal to the spacing of the fMRI you
should get what you want (you can check the fMRI spacing in the
Volumes->Info tab).

> 3)
> and it would also be nice to have an export function to png, eps or some other
> file format?
> for the lightbox-view? (now I have to do a screenshot, and remove the orange
> box (on the top left...) by
> an image manipulation program. )
>

Yes, taking a screenshot with an external utility is our suggested
solution.  Unfortunately I don't know of a way to get rid of the orange
box outlining the selected slice.

> 4)
> it would also be nice if I can specifiy a part of brain to display in the
> lightbox, for example the back part of the brain.
>

Do you mean with pan/zoom?  You can use the right button drag to zoom
and middle button drag to pan.

> 5)
> (It would be also very nice if every of these steps can be done in a batch
> mode or script... are there any plans for such kind of feature?)
>

Sure, everything is scriptable in either python or tcl.  See, for example:

http://www.slicer.org/slicerWiki/index.php/Slicer3:Python

Best regards,
Steve

>
> Andreas
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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