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FSL  October 2018

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Subject:

Re: Orientation Issue

From:

paul mccarthy <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sat, 6 Oct 2018 09:24:13 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (189 lines)

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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