Hi,
If you have swapped LR and SI dimensions then FSLView will show
the axial slices with the left (L) on the left - this is normal.
Re-orienting
to match that of the standard brain is a good idea in this case as it
preserves your left-right labelling correctly (-x y -z is fine for this) and
should keep all the other labels attached to the correct anatomy.
So I would recommend using this fslswapdim command in general.
However, the sform outputs are a bit puzzling. Are you sure that
all you did was apply fslswapdim to
7_ep2d_pace_moco_3DFilter_20080107_0085.nii
which gave you swapped_7_ep2d_pace_moco_3DFilter_20080107_0085.nii.gz?
It is doing what I'd expect in x and z, but not in y. It seems to be
creating an
arbitrary coordinate offset there which I don't normally see. This isn't
necessary a problem, it just creates slightly strange coordinates. Can
you send me the output of fslhd run on these images (and let me know if
any other processing went on)?
On a separate note, it sounds like you are worried about the mm
coordinates. These will not be in standard space if you look at the
first-level outputs. Only the higher-level FEAT outputs are in standard
space. If you want to see your first-level outputs in standard space, then
I recommend using Renderhighres to resample your first-level FEAT
output into standard space, where you will see the usual standard
space coordinates (with negative mm ones).
All the best,
Mark
Emily T Stoneham wrote:
> Hello-
> When I pull up the FSLView image, it shows L on the Left of the image.
> However, I must caveat this: Our scaner flips the Sagittal and the Coronal functionals (the structurals are fine though). When I fix this, that is when I see the change in L R labels in FSL View. The Standard Image from the subject looks fine in FSLView (R on left, L on right side of image). I fixd the sagittal and coronal image by doing this:
> for fn in *.nii ; do fslswapdim $fn -x y -z swapped_$fn ; done
> (I have 290 images that need to be swapped, this fixes them all at once)
>
> The original reason I am trying to straighten this out is that when I am viewing the FEAT data, the voxel and mm data in FSLView is WAY off what it should be. For instance, it will tell me that something clearly in the parietal lobe is actually in the cerebellum. It is as if FSL view doesn't recognize negative values (I never see any except in the mm section, although these aren't right either), and so I figured it was something I did in the inital stages. While trying to figure it out- I noticed the difference in the labelling in FSLView and began to tackle that first off.
>
> Here is the output I got from one image before I swapped it:
> Command: fslorient -getsform 7_ep2d_pace_moco_3DFilter_20080107_0085.nii
> Output: -3 0 0 0 0 3 0 0 0 0 3.17999 0 0 0 0 1
>
> Here is the output I got from one image after I swapped it:
> Command: fslorient -getsform swapped_7_ep2d_pace_moco_3DFilter_20080107_0085.nii.gz
> Output: 3 0 0 -87.9398 0 2.98766 0.288172 -109.99 0 0.271861 -3.1669 73.4814 0 0 0 1
>
> Regards,
> Emily
>
Mark Jenkinson wrote:
> Hi,
>
> How are you determining that the displayed orientation is
> neurological?
> Are the labels right? That is the most crucial thing. The terms
> neurological
> and radiological for display get a bit confusing when the brain is
> not in the
> same orientation as the standard brain.
>
> If the labels are correct (including left and right) then *do not*
> do a fslswapdim
> as that will muck the labels up. I would also avoid using
> fslorient to change
> things unless you know the labels are wrong.
>
> Can you explain more about what you see in FSLView, what you
> expect to see, and
> what the labels are like? Don't worry about the sform values for
> now, although it would
> be helpful to send us the output of fslhd.
>
> All the best,
> Mark
>
>
>
> On 22 Apr 2008, at 19:25, Emily Stoneham wrote:
>
>> Hello all,
>> I have performed an fslorient -getorient, and it tells me it is
>> RADIOLOGICAL, however, when viewed
>> in FSLView, it shows it in Neurological orientation. If I run
>> fslswapdim, I can change that (albeit I get
>> a warning), but I suspect I should be using fslorient to do that
>> instead- (i.e., change the header)?
>> When I run fslorient -getsform, I get a string of numbers, but I
>> don't know what they mean, or
>> how/if I should change one or more (and which) of them. Can you
>> help?
>>
>> Thanks,
>> Emily
>>
>
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