Hi, Flirt people:
I found the answer to Question 1 and 2 by creating images
with pixdim[1] > 0 and pixdim[1] < 0, but kept the data same
I used flsview to see the images. I also used the LR marked
image.
Flirt expects the image to be -1 0 0
0 1 0
0 0 1
It does not matter whether pixdim[1] <0 or >0.
Flirt does not check.
It is good to see that Flirt can handle 90 degree rotation.
Thank you.
Tosa
On Thu, 2003-09-11 at 17:01, Yasunari Tosa wrote:
> HI,
>
> I just downloaded "flirt Version 5.0". I noticed that
> all the images in /etc/standard have pixdim[1] < 0, but
> pixdim[2] and pixdim[3] are positive.
> (Analyze format is so confusing with direction.
> Sometimes, hist.orient is used. You have hist.orient = 0.)
>
> I really appreciate it very much if you could clarify how
> you are using the pixdim[i] to denote the direction cosines.
>
> Question 1:
> ===========
> How are you using this information? Does this mean that
> the direction cosine is of the following form?
> x_r = -1 y_r = 0 z_r = 0
> x_a = 0 y_a = 1 z_a = 0
> x_s = 0 y_s = 0 z_s = 1
> where I denoted RAS(right-anterior-posterior) direction
> of the x, y, z axes component.
>
> What happens if pixdim[1] > 0? Is this the way?
> x_r = 1 y_r = 0 z_r = 0
> x_a = 0 y_a = 1 z_a = 0
> x_s = 0 y_s = 0 z_s = 1
> Or you never use this coordinate system.
>
> Question 2:
> ===========
> Can "flirt" handle the opposite case where e.g pixdim[1] > 0
> where the direction cosine is given by
> x_r = 1 y_r = 0 z_r = 0
> x_a = 0 y_a = 1 z_a = 0
> x_s = 0 y_s = 0 z_s = 1
> (this is the average_305.mnc case where MNI defines
> the orientation stored in the format) ?
>
> Or Do I have to convert the image so that I will have
> pixdim[1] < 0?
>
> Depending on these, left and right are flipped.
>
> Question 3:
> ===========
> Can "flirt" handle the general cases where the direction cosine
> of the src is, e.g.in the coronal direction but the reference is
> in the horizontal direction (LAS or RAS) ?
>
> Thank you in advance for your reply
>
> Tosa
> ====================================================
> Yasunari Tosa, Ph.D.
> R&D Enginner email: [log in to unmask]
> Mass. General Hospital NMR Center phone:
> Building 149
> 13th Street fax :
> Charlestown, MA 02129
--
Yasunari Tosa, Ph.D.
R&D Enginner email: [log in to unmask]
Mass. General Hospital NMR Center phone:
Building 149
13th Street fax :
Charlestown, MA 02129
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