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Subject:

Re: diplaying NIFTI images

From:

Graham Wideman <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 21 Oct 2004 03:23:49 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (56 lines)

Lazar:

Couple of points, neither specifically related to NIFTI, but perhaps helpful.

1. What do you mean by the orientation of your data "corresponding to
the neurological one."

Strictly speaking, this is a little off-target -- neurological vs radiological conventions are *viewing* issues, not data-order issues.
It is up to the viewer software to present the data to you in
one or other of those preferred views regardless of order of data in the file.

That said, it does appear to be the case that due to intractable viewers in the past, some data users have developed customs where they rearranged the order of data in their data files to get it to show in the viewer the way they want --
but that's "fixing" the problem by introducing another problem.

In NIFTI, you can store the data in any of 48 different orders, which might
be described as (L-R, S-I, A-P) or (I-S, P-A, L-R) and so on (48 different permutations).

But so long as the NIFTI header info describes the image data order
correctly, you as the user would be unaware of the data order because the
viewer should simply present it correctly. And if that viewer is set to show
data in radiological view, it will do that regardless of NIFTI data order.

2. In order to troubleshoot these puzzles it can be useful to have a
viewer that knows nothing about header info, and simply shows you the raw
data in its raw order. One such example is available at my site:

http://wideman-one.com/gw/brain/tools/gworc/index.htm

3. And obviously the above story is further modified for viewers that can rotate and interpolate in 3D, and are not merely showing slices along one of the three "data axes".

Hope that helps,

Graham


At 10/20/2004 09:56 PM, you wrote:
>Hello,
>
>
>I have created an img/hdr NIFTI pair with orientation corresponding to
>the neurological one. Because such files look like analyze pair, the old
>and the new FSLview can display the images. I would, however, expect
>different image orientations because analyze coordinate system is fixed
>where as NIFTI supports directional cosines.
>
>What bothers me is that old FSLview (1.0 beta 7) and the new one (2.3.5)
>produce exactly the same displays.
>
>Are not I correct in my expectations? I do not understand what I am
>missing.
>
>
>Thank you for your kind help,
>
>Lazar

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