Dear Farzaneh,
>
> To apply "eddy" on diffusion images, I use "fslmerge" according to the procedure explained in fslwiki. Although all of my data was acquired in a same way, I get the following warning for some of them.
>
> fslmerge -t A2P_P2A_B0 A2P_B0 HARDI_B0
>
> WARNING:: Inconsistent orientations for individual images when attempting to merge.
> Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
>
> I checked the fslhd for the two images (A2P_B0, HARDI_B0) and as it can be found in the attachments, all qform and sform orientations are the same. Since I get this warning for some of date, I'm wondering what is wrong and how I could fix it.
> I really appreciate your kind help.
when looking at your q/sforms I see that it looks like there is a translation difference between your two volumes. I am guessing these differences must have been created by your dicom->nifti conversion, presumably because of something in the original dicoms.
Does fslmerge still produce a merged output? If so, I think you can ignore the warning (though it might still be useful for you to hunt down why it occurs in the first place). Even if there is a translational difference of the images that correspond to that of the s/qforms, topup and/or eddy have movement models that should be able to detect and correct for this difference.
Jesper
>
> Best Regards
> Farzaneh
> filename A2P_B0.nii.gz
>
> sizeof_hdr 348
> data_type INT16
> dim0 3
> dim1 128
> dim2 128
> dim3 68
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.000000
> pixdim1 2.000000
> pixdim2 2.000000
> pixdim3 2.000000
> pixdim4 9.000000
> 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 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 -1.994661 0.048748 0.137660 123.276016
> qto_xyz:2 -0.022610 1.759467 -0.950665 -84.046516
> qto_xyz:3 0.144275 0.949684 1.754219 -87.032860
> 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 -1.994661 0.048748 0.137663 123.276016
> sto_xyz:2 -0.022610 1.759467 -0.950665 -84.046516
> sto_xyz:3 0.144278 0.949684 1.754219 -87.032860
> 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 FSL5.0
> aux_file
>
>
> filename HARDI_B0.nii
>
> sizeof_hdr 348
> data_type INT16
> dim0 3
> dim1 128
> dim2 128
> dim3 68
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.000000
> pixdim1 2.000000
> pixdim2 2.000000
> pixdim3 2.000000
> pixdim4 9.000000
> pixdim5 1.000000
> pixdim6 1.000000
> pixdim7 45718.199219
> 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 -1.995257 -0.000000 0.137661 126.385292
> qto_xyz:2 -0.065591 1.758389 -0.950665 -81.227844
> qto_xyz:3 0.121031 0.952925 1.754219 -85.749336
> 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 -1.995257 0.000000 0.137663 126.385292
> sto_xyz:2 -0.065591 1.758389 -0.950665 -81.227844
> sto_xyz:3 0.121032 0.952925 1.754219 -85.749336
> 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
> aux_file
>
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