Hi Georg,<div><br></div><div>I've just had a look into your issue, and I can confirm that there is indeed a tiny little bug, but not in the conversion to NIfTI. The problem is purely in the display of the ROI, the images themselves are fine.</div>
<div><br></div><div>For those who are interested, it's due to the fact that the transform information is stored differently in NIfTI than it is in MRtrix, leading to tiny rounding errors between the transform matrices when loaded in MRtrix. The part of the code responsible for displaying the ROI first checks whether the ROI's transform is identical to the main image, and if not, will regrid the ROI image to match. That regridding is obviously not perfect, and leads to the funny mismatch in the overlay that you've observed. </div>
<div><br></div><div>I've got a fix for that for those who are bothered by this. Basically it will now allow minor differences (less than 10e-5) between elements of the transform matrices, which seems to fix the issue at least in the test data that I tried it on... To apply the fix, overwrite the src/mrview/sidebar/roi_analysis/roi_list.cpp file with the attached, issue the ./build command and proceed as usual. Otherwise, the fix will be included in the next version, which is due for release fairly soon anyway.</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br><br><div class="gmail_quote">On 29 September 2011 16:54, Georg Kerbler <span dir="ltr"><<a href="mailto:g.kerbler@uq.edu.au">g.kerbler@uq.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi,<br>
<br>
When I used fa.mif (instead of fa.nii) it worked, thanks for that suggestion Rene!<br>
So it seems to be a problem with the conversion from .mif to .nii<br>
<br>
cheers,<br>
georg_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: +61 (0)3 9035 7033<br>
</div>