Hi,
The answer to this depends on what the problem with the orientations is.
This warning sometimes occurs due to very small changes in the mm coordinate
system (often associated with shifts in the subject wrt the magnetic isocentre).
However, it can also occur when the orientation changes are dramatic, such
as a left-right flip. In the former case you don't need to do anything, but if it is
the latter - and it sounds like it is - then you need to get everything in the
same orientation before performing fslmaths commands.
Normally a mask will have the same information as the image from which it
was derived. If this is not the case then you can try using fslorient with the
-swaporient option and see if that fixes the problem - but be *very* careful
to view the images before and after running fslorient to check that it does
not cause the mask to be swapped incorrectly (check that the labels are
correct for the mask). It is difficult to say, without knowing how the mask
was created, whether the mask orientation is currently correct or not.
Hence I do not know whether the use of fslorient will fix the problem by
itself or not. It may require the use of fslswapdim as well, if fslorient does
not do the right thing.
Sorry the answer is not easier, but it really depends on how the mask
was created, what the orientation problem is, and what it looks like in
fslview. Try using fslorient on the images to start with (without the
-swaporient option) just to see what orientation they currently have. If
it is different then try running fslorient with -swaporient on the mask.
Then check this in fslview and see if the result is correct or not wrt
the labels. If it is the wrong way around the try using fslswapdim to
correct it.
Hopefully this will get things working for you.
If you are still stuck then email us again.
All the best,
Mark
On 18 Mar 2011, at 19:55, WangPing wrote:
> and how to make two nifti images the consistent orientations? thanks
>
> Date: Sat, 19 Mar 2011 03:43:48 +0800
> From: [log in to unmask]
> Subject: [FSL] question about fslmaths -mas
> To: [log in to unmask]
>
> dear fsl list:
>
> sorry to bother.
> I have a nifti image and a mask image, both looks correct with mricro, however when I use the following command line:
>
> "fslmaths in_img -mas mask_img out_img"
>
> it prompted the following warning message:
> ===
> WARNING:: Inconsistent orientations for individual images in pipeline!
> Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
> ====
> and looks like the out_img was flipped (left and right), does anyone know how to fix this problem?
>
> Best,
> ping wang
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