Dear Joyce,
There are some small differences in the location of the origin in the
two scans (see the last column in the sform and qform matrices).
This seems surprising if the filteredfunc_post was derived from the
filteredfunc_pre (as only our spatial tools, like flirt/fnirt/applywarp)
will change the origin information. However, if they are derived
from different scans (same individual in the same or different sessions)
then it is easy to get a different origin, but you should do registration
between the images before running fslmaths in this case. The
registration step will fix the differences in the sform/qform matrices.
Alternatively, if you are sure that these images are aligned correctly
then you can continue with your processing and ignore the warning.
However, it does normally indicate that something is being run on
images that have not been registered when they should have been.
So check carefully, and if you want clarification then just let us know
how these images were created, as that is what is important in these
cases.
All the best,
Mark
On 18 Dec 2011, at 20:28, Joyce Chen wrote:
> Dear FSL,
>
> I saw a few posts on this warning message, but I still was unable to resolve my question.
>
> I ran: fslmaths filteredfunc_post -sub filteredfunc_pre output (as I wanted to get a difference image to use for higher level feat analyses).
>
> This was the warning message I got: inconsistent orientations for individual images in pipeline. Will use voxel-based orientation which is probably incorrect. please check.
>
> I looked at the header info for both files and did not notice any differences (see below, they are identical), so I'm not sure why I am getting this error, and/or if I am doing something wrong.
>
> Thanks for any advice you have.
>
> Joyce
>
>
> for the pre file:
> filename filtered_func_data.nii.gz
>
> sizeof_hdr 348
> data_type FLOAT32
> dim0 4
> dim1 64
> dim2 64
> dim3 28
> dim4 294
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 3.7500000000
> pixdim2 3.7500000000
> pixdim3 5.0000000000
> pixdim4 2.0000000000
> 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 Scanner Anat
> qform_code 1
> qto_xyz:1 -3.750000 0.000000 -0.000000 118.125000
> qto_xyz:2 0.000000 3.750000 -0.000000 -79.957001
> qto_xyz:3 0.000000 0.000000 5.000000 -43.356400
> 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 -3.750000 0.000000 0.000000 118.125000
> sto_xyz:2 0.000000 3.750000 0.000000 -79.957001
> sto_xyz:3 0.000000 0.000000 5.000000 -43.356400
> 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 FSL4.1
> aux_file
>
>
>
> File for post:
>
> filename filtered_func_data.nii.gz
>
> sizeof_hdr 348
> data_type FLOAT32
> dim0 4
> dim1 64
> dim2 64
> dim3 28
> dim4 294
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 3.7500000000
> pixdim2 3.7500000000
> pixdim3 5.0000000000
> pixdim4 2.0000000000
> 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 Scanner Anat
> qform_code 1
> qto_xyz:1 -3.750000 0.000000 -0.000000 118.857002
> qto_xyz:2 0.000000 3.750000 -0.000000 -79.225998
> qto_xyz:3 0.000000 0.000000 5.000000 -47.746700
> 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 -3.750000 0.000000 0.000000 118.857002
> sto_xyz:2 0.000000 3.750000 0.000000 -79.225998
> sto_xyz:3 0.000000 0.000000 5.000000 -47.746700
> 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 FSL4.1
> aux_file
>
|