Dear Cinly,
If you are including the (0,0,0) voxel in your ROI then there should
be no change to the sform or qform. If you are starting a min
voxel that is non-zero then it should modify the qform and sform
to account for this. However, I just noticed in my quick test that
it is not doing that, so this is a small bug that we need to fix.
Currently it leaves the qform and sform unchanged, which preserves
the left-right orientation, but will mean that the mm coordinates
associated with voxel locations will change. We will get onto that
and have a patch out soon for this.
In the meantime you can work out the appropriate sform or qform
and modify them with fslorient. The formula that should have
been applied in the code is:
new_qform = old_qform * shiftmat
where shiftmat = [ 1 0 0 xmin ; 0 1 0 ymin ; 0 0 1 zmin ; 0 0 0 1]
(matlab notation - which I hope it clear).
This has the effect of taking the new voxel at the (0,0,0) location
and effectively shifting its voxel coordinates to be (xmin,ymin,zmin)
as it used to be prior to the fslroi call, and hence then the old
qform can be used. The formula is the same for the sform.
Not sure what you were expecting to see with FLIRT. As you've
started at (0,0,0) for your ROI I wouldn't expect any change
as the formula above keeps the qform and sform the same.
All the best,
Mark
On 7 Sep 2011, at 22:09, Cinly Ooi wrote:
> Dear FSL,
>
> I am trying to use the BET2-FAST-FLIRT pipeline on MPRAGE (3D structural) data. As part of the process, I need to remove the neck using fslroi before BET2.
>
> My question is how does using fslroi to crop the image affect the sform and qform code? The specific instruction I changed using fslroi is y-axis, ymin=0, ysize=175 (original is 240).
>
> Since FSL website make a big effort to document Left/right flip on fslorient and other tools [Thank you for doing this. I deeply appreciated this], I am pretty sure the fact that you did not mention anything about L-R flip and qform/sform code means there is no effect at all.
>
> I pushed the data through FLIRT and cannot see any difference on FLIRT output.
>
> Many thanks in advance and Best Regards,
> Cinly
>
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