Mark,
Before the image was swapped, I converted the DICOM in MRIconvert to FSL NIFTI format. Beyond that, the only processing done at this point is the swapping of the sagittal image. Here is the output from fslhd on one of the swapped images (below).
Thanks!
Emily
Byte swapping
filename swapped_7_ep2d_pace_moco_3DFilter_20080107_0001.nii.gz
sizeof_hdr 348
data_type INT16
dim0 3
dim1 64
dim2 64
dim3 48
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 3.1799850464
pixdim4 0.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 2
freq_dim 1
slice_dim 3
slice_name alternating_increasing
slice_code 3
slice_start 0
slice_end 47
slice_duration 0.040000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 3.000000 -0.000000 -0.000000 -87.939758
qto_xyz:2 0.000000 2.987657 0.288172 -109.990044
qto_xyz:3 0.000000 0.271861 -3.166901 73.481400
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Superior-to-Inferior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 3.000000 0.000000 0.000000 -87.939758
sto_xyz:2 0.000000 2.987657 0.288172 -109.990044
sto_xyz:3 0.000000 0.271861 -3.166901 73.481400
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Left-to-Right
sform_yorient Posterior-to-Anterior
sform_zorient Superior-to-Inferior
file_type NIFTI-1+
file_code 1
descrip FSL4.0
----- Original Message -----
From: Mark Jenkinson <[log in to unmask]>
Date: Wednesday, April 23, 2008 11:02 am
Subject: Re: [FSL] Header data
> 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'tnecessary 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
> standardspace. 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
> >>
> >
>
|