Hi Markus,<div><br></div><div>csdeconv outputs one 'failure to converge' message per voxel where the maximum number of CSD iterations was exceeded (by default, the maximum is 50 iterations). So unless you're getting thousands of these messages, the proportion of affected voxels is probably fairly low. Moreover, these issues typically arise in GM or CSF, without affecting WM voxels. Finally, even in affected voxels, this is usually not a problem, as what generally happens is that the algorithm oscillates between two equally good solutions. If you allow the program to run to completion and inspect the resulting FODs in MRView (orientation plot sidebar with overlay), my guess is the results will look OK.</div>
<div><br></div><div>You'll get bigger problems if you get "not enough negative directions" messages. In these cases, the affected voxels are assigned a NaN value, and so can't be tracked through. Note this only happens when using super-resolution (i.e. lmax is greater than the data can natively support). </div>
<div><br></div><div>Hope that helps.</div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br></div><div><div class="gmail_quote">On 20 December 2011 09:34, Markus Gschwind <span dir="ltr"><<a href="mailto:markus.gschwind@gmail.com">markus.gschwind@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear experts,
<div><br></div><div>I'd like to ask what could be the reasons whay csdeconv fails and gives an error like </div><div><br></div><div><div>> csdeconv data.mif response.txt -mask mask.nii -grad gradtable.txt CSDm.mif</div>
<div>csdeconv: performing constrained spherical deconvolution... Â 0%csdeconv: failed to converge</div><div>csdeconv: failed to converge</div><div>csdeconv: failed to converge</div><div>csdeconv: failed to converge</div>
<div>
csdeconv: failed to converge</div></div><div>csdeconv: failed to converge</div><div>csdeconv: failed to converge</div><div>etc.</div><div><br></div><div>I tried with different -lmax and with different thresholded sf.mif (values 0.7, 0.6, 0.5, 0.4).</div>
<div><br></div><div>Principally the commands are correct as they worked with other brains, but not with the one in question ( a lesioned one does it not work with brain lesions?).</div><div>How should I proceed best  in order to debug?</div>
<div><br></div><div>Thanks in advance!</div><span class="HOEnZb"><font color="#888888"><div>Markus</div>
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<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>
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