Hi Krista,
If you can load all masks on top of one another in FSLView, and are happy with that, then you can probably just ignore the warning from fslmerge.
Otherwise, send us the information about the dimensions (dim1 to dim3 and pixdim1 to pixdim3).
All the best,
Mark
On 1 Mar 2013, at 22:26, krista kelly <[log in to unmask]> wrote:
> Hi all,
>
> I have 3 Proton Density masks that were created on different computers using FSLview and for some reason I cannot merge these masks together. Although the orientations look correct within FSLview and I am able overlay all masks on top of one another, when I try to merge the masks together, I get the following warning:
>
> <<<Inconsistent orientations for individual images when attempting to merge.>>>
>
> fslhd info shows different q and sform orientations between masks
>
> mask 1 and 2:
> qform_xorient Right-to-Left
> qform_yorient Inferior-to-Superior
> qform_zorient Anterior-to-Posterior
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 -0.374352 0.021748 -0.004721 91.568634
> sto_xyz:2 0.006226 0.046610 -0.496053 19.196569
> sto_xyz:3 0.021137 0.371456 0.062521 -99.225533
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Inferior-to-Superior
> sform_zorient Anterior-to-Posterior
>
> Mask2:
> qform_xorient Right-to-Left
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name Aligned Anat
> sform_code 2
> sto_xyz:1 -0.375000 0.000000 0.000000 96.375000
> sto_xyz:2 0.000000 0.375000 0.000000 -90.375000
> sto_xyz:3 0.000000 0.000000 0.500000 -32.000000
> 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
>
> When I use fslswapdim to change orientations between planes (e.g. fslswapdim <infile> RP IS AP <outfile>) the mask is totally flipped around in orientation when I open it using FSLview and it cannot be overlaid on top of the other masks.
>
> Does anyone know how to approach this problem?
>
> Thanks!
> Krista
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