Hi Cecile,
What you are initially seeing is the image data as it is stored in the
file, i.e. its orientation in voxels.
As long as the anatomical labels are correct, it is generally not a
problem to have a strange voxel orientation.
But it is generally a good idea to run fslreorient2std on all of your
images, as this will improve the chances that the registration steps
will succeed.
Paul
On 25/07/2019, Cecile Madjar <[log in to unmask]> wrote:
> Hello,
>
> When I open my NIfTI file using fsleyes, I see the images displayed upside
> down (with the top of the head and the label S at the bottom of the
> application instead of the top).
>
> If I select "World coordinates" in the display space, then the head is
> correctly displayed with the top of the head and the S label at the top of
> the screen. I wanted to attach images to illustrate but my previous post was
> rejected because of the size of the post.
>
> I am not sure why I observe this behaviour on the NIfTI files I have. Do you
> have any idea why I experience this?
>
> Thank you for your help.
> Best,
>
> Cécile
>
> PS: in case that is helpful, here is the header information I obtain when
> running fslhd on the same file
>
> size of header 348
> data_type FLOAT32
> dim0 3
> dim1 176
> dim2 240
> dim3 256
> dim4 0
> dim5 0
> dim6 0
> dim7 0
> vox_units Unknown
> time_units Unknown
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.000000
> pixdim1 1.000000
> pixdim2 1.000000
> pixdim3 1.000000
> pixdim4 0.000000
> pixdim5 0.000000
> pixdim6 0.000000
> pixdim7 0.000000
> vox_offset 352
> cal_max 0.000000
> cal_min 0.000000
> scl_slope 0.000000
> 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
> toffset 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 1
> sto_xyz:1 0.999353 -0.011709 -0.034021 -88.706795
> sto_xyz:2 -0.011703 -0.999931 0.000398 142.143250
> sto_xyz:3 -0.034023 0.000000 -0.999421 101.400314
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Left-to-Right
> sform_yorient Anterior-to-Posterior
> sform_zorient Superior-to-Inferior
> file_type NIFTI-1+
> file_code 1
> descrip mnc2nii
> /data/preventad/data//assembly/1004359/PREBL00/mri/processed/MINC_defac
> aux_file
>
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