Hi,
This is as I thought.
Your 44x44x44 image has 1x1x1mm voxel size (pixdim1-3)
and hence the whole image is only 44x44x44mm in size.
Therefore resampling this to the 256x191x256 image doesn't
alter the size as the voxels are still 1x1x1mm and so it sits
down in the bottom corner.
You need to correctly specify the voxel size in the image
sloreta.nii. The voxel size can be changed with fslchpixdim.
Once that is done then the previous flirt command should
do the correct resampling.
All the best,
Mark
On 31 Jan 2009, at 13:41, Veronique Weser wrote:
> Thank you.
>
> Here is the header information of the high and low res images:
>
>
> HI-RES FILE:
>
> fslhd NY59_preop_swap.nii.gz filename NY59_preop_swap.nii.gz
>
> sizeof_hdr 348
> data_type INT16
> dim0 3
> dim1 256
> dim2 191
> dim3 256
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 0.8984375000
> pixdim2 1.0000000000
> pixdim3 0.8984375000
> pixdim4 1.0000000000
> 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 0
> freq_dim 0
> slice_dim 0
> slice_name Unknown
> slice_code 0
> slice_start 0
> slice_end 0
> slice_duration 0.000000
> 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 Unknown
> qform_code 0
> qto_xyz:1 0.898438 0.000000 0.000000 0.000000
> qto_xyz:2 0.000000 1.000000 0.000000 0.000000
> qto_xyz:3 0.000000 0.000000 0.898438 0.000000
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Left-to-Right
> 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 FSL4.0
> aux_file
>
>
> LOW-RES FILE:
>
> fslhd sloreta.nii
> filename sloreta.nii
>
> sizeof_hdr 348
> data_type FLOAT32
> dim0 3
> dim1 44
> dim2 44
> dim3 44
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.0000000000
> pixdim4 3.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 352
> cal_max 0.0728
> cal_min 0.0000
> scl_slope 1.000000
> scl_inter 0.000000
> phase_dim 0
> freq_dim 0
> slice_dim 0
> slice_name Unknown
> slice_code 0
> slice_start 0
> slice_end 0
> slice_duration 0.000000
> 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 Unknown
> qform_code 0
> qto_xyz:1 1.000000 0.000000 0.000000 0.000000
> qto_xyz:2 0.000000 1.000000 0.000000 0.000000
> qto_xyz:3 0.000000 0.000000 1.000000 0.000000
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Left-to-Right
> 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 FSL4.0
> aux_file
>
>
> --- On Sat, 1/31/09, Mark Jenkinson <[log in to unmask]> wrote:
> From: Mark Jenkinson <[log in to unmask]>
> Subject: Re: [FSL] image scaling
> To: [log in to unmask]
> Date: Saturday, January 31, 2009, 2:24 AM
>
> Hi,
>
> What are the voxel sizes of your images?
> From what you've shown it looks like your voxel size (in mm) has not
> also changed resolution. For instance, if the 182x218x182 image has
> 1mm cubic resolution then I'd expect the 44x44x44 image to have
> 4 to 5 mm cubic resolution. If this is not the case (and the 44x44x44
> image has 1mm voxel
> sizes) then you'd get what you show.
>
> If this isn't the case, please send the results of fslhd run on each
> of your images.
>
> All the best,
> Mark
>
>
>
>
> On 31 Jan 2009, at 03:05, Veronique Weser wrote:
>
> > Thank you.
> >
> > When I try this, the low res image gets converted to the higher
> resolution. but when I load both the high and low res images into
> fslview
> together, the actual nonzero voxels I am interested in stay in the
> lower corner
> of the image. That is, the activation image I am trying to 'blow up'
> does not change its actual size.
> > If that doesn't make any sense, I have attached a screenshot to
> better
> explain it. The cursor is on the low res image (which is an
> activation image
> that I want to overlay), the big brain you see is the high res image.
> > Any suggestions?
> >
> > Thanks!
> >
> > --- On Fri, 1/30/09, Matt Glasser <[log in to unmask]>
> wrote:
> > From: Matt Glasser <[log in to unmask]>
> > Subject: Re: [FSL] image scaling
> > To: [log in to unmask]
> > Date: Friday, January 30, 2009, 6:39 PM
> >
> > flirt –in <lowres> –ref <hires> –applyxfm –out
> <lowresNOWAThires>
> >
> >
> > Depending on the type of data you might want to keep the default of
> trilinear interpolation, or use nearest neighbor interpolation.
> >
> >
> > Peace,
> >
> >
> > Matt.
> >
> >
> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Veronique Weser
> > Sent: Friday, January 30, 2009 8:33 PM
> > To: [log in to unmask]
> > Subject: [FSL] image scaling
> >
> >
> >
> > Dear List,
> >
> > I have two images which are supposedly in the same space, with the
> difference being that one image has a resolution of 182x218x182 and
> the
> other
> 44x44x44. Is there any way to scale/upsample the lower resolution
> image to the
> higher resolution image (i.e. 'blowing' up the low res image)?
> >
> > Thanks a lot,
> >
> > Veronique
> >
> >
> >
> > <scaling1.jpg>
>
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