Hi,
Here it is:
Thanks!
Emily
filename 7_ep2d_pace_moco_3DFilter_20080107_0001.nii
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 Unknown
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 101.060242
qto_xyz:2 0.000000 2.987657 -0.288172 -96.445969
qto_xyz:3 0.000000 0.271861 3.166901 -75.362930
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip ep2d_pace_moco_3DFilter
aux_file
----- Original Message -----
From: Mark Jenkinson <[log in to unmask]>
Date: Wednesday, April 23, 2008 5:30 pm
Subject: Re: [FSL] Header data
> Hi,
>
> I need the output from fslhd on both of the images to see what has
> happened.
> I suspect that you have sform_code=0 and qform_code=1 before you do
> theswap, but I really want to check. Can you please send me the
> fslhd from
> both images?
>
> All the best,
> Mark
>
>
>
> On 23 Apr 2008, at 16:21, Emily T Stoneham wrote:
>
> > 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
> >>>>
> >>>
> >>
> > <estoneha.vcf>
>
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