Dear Stephen, John,
Thanks for your help! My main problem was that I did not realize images
could be flipped within the display window (rotating by x degrees would not
be sufficient to realign the images). However it appears that resizing along
an axis by -1 essentially flips the image. Is this correct?
Rachael
Rachael D. Seidler, PhD
University of Minnesota Dept of Neuroscience
and Brain Sciences Center (11B)
Veterans Affairs Medical Center
One Veterans Drive
Minneapolis, MN 55417
Phone: 612 725-2000 x.1765
Fax: 612 725-2291
Email: [log in to unmask]
>From: "Stephen Fromm" <[log in to unmask]>
>To: "Rachael Seidler" <[log in to unmask]>
>Subject: Re: more on image orientation
>Date: Wed, 26 Jul 2000 12:04:27 -0400
>
>Dr. Seidler:
>
> > I know orientation has been covered quite a bit already, but could not
>find
> > this specific issue in the archives:
> > My data is in axial slices that require the following flips to bring
>them
> > into radiological orientation:
> > sagittal images must be flipped horizontally
> > axial images must be flipped vertically.
>
>I think what you mean is that you have axial slices, and that if you take a
>sagittal *view* of the entire volume of axial slices, you must "flip the
>view" horizontally.
>
> > I perform these flips in stimulate software before converting to analyze
> > file format. When I display these axial slices in spm, the sagittal and
> > coronal reconstructions are upside down.
> > In an attempt to correct this, I changed the affine norm etimates during
> > spatial normalization to -1, -1, -1. However, when I try to display
>these
> > images, I get a blank display window. How can I check the images to
> > determine whether they are in the proper orientation? Is this the
>correct
> > fix?
>
>I don't know about the blank window business; that's strange.
>
>Here's how I would do it, assuming you're using SPM99.
>
>(1) You might as well do it all in SPM; don't bother with the Stimulate
>steps.
>(2) First, pick one of the volumes and display it using the Display button.
>(3) Second, using the rotation fields in the Display window, flip the image
>around until it looks right:
>
>in Neurological orientation, that would be
>-------------------------------------------------
>| Superior | Superior |
>| | |
>|Left Right | Anterior Posterior |
>| | |
>| Inferior | Inferior |
> -------------------------------------------------
>| Anterior |
>| |
>|Left Right |
>| |
>| Posterior |
> ---------------------
>
>In radiological orientation, that would be
>
> -------------------------------------------------
>| Superior | Superior |
>| | |
>|Right Left | Anterior Posterior |
>| | |
>| Inferior | Inferior |
> -------------------------------------------------
>| Anterior |
>| |
>|Right Left |
>| |
>| Posterior |
> ---------------------
>
>Now, there *may* be some method to reverse right-and-left, to switch from
>neurological to radiological (or vice versa), but I forget. You *cannot*
>do
>it by rotations alone, of course.
>
>But that really doesn't matter, as long as you keep track. The only place
>in SPM I know of where it matters is at the normalization stage. The
>default (set in spm_defaults.m) is to assume the images to be normalized
>are
>radiological. So if your images are rad'l, you're fine. If they're
>neurological, you can change the setting in the Normalization area of the
>defaults editing window (press the defaults button). You have to do this
>every time you start up spm99, though; if you want it to persist across
>sessions, you'd have to edit the spm_defaults.m file with a text editor.
>You don't need to worry about it if you're doing things unrelated to
>normalization.
>
>Finally, to reorient all your images, there are buttons in the display
>window to do this. I think it's something like "reorient images". This
>doesn't actually change the images themselves (*.hdr or *.img). Rather, it
>creates a *.mat file with the flipping information in it. Subsequent
>actions in SPM99 will read this file before doing anything with the images.
>
>Best wishes,
>
>Stephen Fromm, PhD
>NIDCD/NIH
>
>
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