Hi Laura,
The qto_xyz/sto_xyz differences are normal and to be expected. The
differenes in the pixdim fields are less common, but can happen
occasionally. You will probably need to update the pixdims in your
images to match your acquisition parameters (e.g. change 5.000175 to
5.0, and 2.007500 to 2.0) - you can use fsledithd to do this.
There will always be differences in the sform and qform (qto_xyz and
sto_xyz) across different scans - this will depend on the scanner
field-of-view set up. The left-right flip (one being neurological and
the other radiological) is strange, but can happen, and again will be
due to the scanner set up.
But if, when you open these images in FSLeyes/FSLView, the anatomical
labels are correct, then these differences are nothing to worry about.
A recommended step for all images as they come off the scanner is to
use fslreorient2std on them to change their orientation to match the
MNI152 template (without any registration or resampling). This won't
make their qforms/sforms the same, but it will make the left-right
orientations consistent, which can help in subsequent processing.
Cheers,
Paul
On 01/10/2018, SUBSCRIBE FSL Laura Dennis <[log in to unmask]> wrote:
> Hello,
>
> Below is the "fslhd" output for two different subjects supposedly acquired
> the same way but they have many discrepancies between the two. Also, when I
> run fslorient, one says radiological and the other neurological. My
> anatomical scans are also neurological.
>
> Can you help me with the correct commands to fix this issue?
>
> Thanks!
>
>
> [Laura@hoffmanlab1 raw]$ fslhd MND883.PDD.EPI1.nii.gz
> filename MND883.PDD.EPI1.nii.gz
>
> sizeof_hdr 348
> data_type UINT16
> dim0 4
> dim1 128
> dim2 128
> dim3 24
> dim4 615
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 512
> nbyper 2
> bitpix 16
> pixdim0 0.000000
> pixdim1 1.875000
> pixdim2 1.875000
> pixdim3 5.000175
> pixdim4 2.007500
> pixdim5 0.000000
> pixdim6 0.000000
> pixdim7 0.000000
> 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_2
> slice_code 5
> slice_start 0
> slice_end 23
> 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 Scanner Anat
> qform_code 1
> qto_xyz:1 -1.874772 -0.000076 -0.078002 119.156219
> qto_xyz:2 -0.000076 -1.874975 0.025999 126.650688
> qto_xyz:3 -0.029250 0.009749 4.999499 -33.689903
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Anterior-to-Posterior
> 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 PDD_EPI
> aux_file
>
>
>
> [Laura@hoffmanlab1 raw]$ fslhd MND391.PDD.EPI1.nii.gz
> filename MND391.PDD.EPI1.nii.gz
>
> sizeof_hdr 348
> data_type INT16
> dim0 4
> dim1 128
> dim2 128
> dim3 24
> dim4 615
> dim5 0
> dim6 0
> dim7 0
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.000000
> pixdim1 1.875000
> pixdim2 1.875000
> pixdim3 5.000000
> pixdim4 2.000000
> pixdim5 0.000000
> pixdim6 0.000000
> pixdim7 0.000000
> 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_2
> slice_code 5
> 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 Scanner Anat
> qform_code 1
> qto_xyz:1 -1.871899 -0.000000 0.287423 119.450554
> qto_xyz:2 -0.005650 1.872422 -0.261680 -93.772369
> qto_xyz:3 0.107635 0.098292 4.984868 -54.215023
> 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 Scanner Anat
> sform_code 1
> sto_xyz:1 -1.871899 -0.000000 0.287426 119.450554
> sto_xyz:2 -0.005650 1.872422 -0.261680 -93.772369
> sto_xyz:3 0.107636 0.098292 4.984868 -54.215023
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip TE=38;Time=102955.485;phase=1;dwell=0.460
> aux_file
>
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