Hi all,<div><br></div><div>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:</div>
<div><br></div><div><div>&lt;&lt;&lt;Inconsistent orientations for individual images when attempting to merge.&gt;&gt;&gt;</div></div><div><br></div><div>fslhd info shows different q and sform orientations between masks</div>
<div><br></div><div>mask 1 and 2:</div><div><div>qform_xorient  Right-to-Left</div><div>qform_yorient  Inferior-to-Superior</div><div>qform_zorient  Anterior-to-Posterior</div><div>sform_name     Scanner Anat</div><div>sform_code     1</div>
<div>sto_xyz:1      -0.374352  0.021748  -0.004721  91.568634</div><div>sto_xyz:2      0.006226  0.046610  -0.496053  19.196569</div><div>sto_xyz:3      0.021137  0.371456  0.062521  -99.225533</div><div>sto_xyz:4      0.000000  0.000000  0.000000  1.000000</div>
<div>sform_xorient  Right-to-Left</div><div>sform_yorient  Inferior-to-Superior</div><div>sform_zorient  Anterior-to-Posterior</div></div><div><br></div><div>Mask2:</div><div><div>qform_xorient  Right-to-Left</div><div>qform_yorient  Posterior-to-Anterior</div>
<div>qform_zorient  Inferior-to-Superior</div><div>sform_name     Aligned Anat</div><div>sform_code     2</div><div>sto_xyz:1      -0.375000  0.000000  0.000000  96.375000</div><div>sto_xyz:2      0.000000  0.375000  0.000000  -90.375000</div>
<div>sto_xyz:3      0.000000  0.000000  0.500000  -32.000000</div><div>sto_xyz:4      0.000000  0.000000  0.000000  1.000000</div><div>sform_xorient  Right-to-Left</div><div>sform_yorient  Posterior-to-Anterior</div><div>
sform_zorient  Inferior-to-Superior</div></div><div><br></div><div>When I use fslswapdim to change orientations between planes (e.g. fslswapdim &lt;infile&gt; RP IS AP &lt;outfile&gt;) 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. </div>
<div><br></div><div>Does anyone know how to approach this problem?</div><div><br></div><div>Thanks!</div><div>Krista</div>