Hi Nyoman,<div><br></div><div>To be honest, I don't recommend ever using it. Normalising to the b=0 image might be appealing since it should in theory provide more quantitative information, but in practice it introduces more errors than it fixes, since even a tiny amount of partial voluming with CSF will cause a big drop in the normalised DW signal, and hence in the normalised FOD. Also, to use it correctly, you'd need to supply a 'normalised' response function, for example one that you might have derived using an axially symmetric tensor model. I expect you used the data-derived response function, and that this is probably the reason why your FODs were so small. You could use them for tracking, but you'd have to use a much lower -cutoff than the default value of 0.1, since the scaling will be off by roughly the b=0 signal amplitude.</div>
<div><br></div><div>In any case, you shouldn't need to normalise if you're using a response function derived from the same data (as per the documentation) since the response function will also be appropriately scaled to the DW signal, and the spherical deconvolution output will therefore inherently be normalised. This way, your FODs won't be artificially reduced in regions adjoining CSF, although you may then have to worry about intensity variations if you have a significant bias field in your images.<br>
<br>Cheers,</div><div><br></div><div>Donald.</div><div><br><br><div class="gmail_quote">On 27 July 2012 13:02, Nyoman Kurniawan <span dir="ltr"><<a href="mailto:nyoman.kurniawan@cai.uq.edu.au" target="_blank">nyoman.kurniawan@cai.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">
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<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Dear Dondald,<br>
Would you be able to tell us when to use the option -normalise in csdeconv?<br>
If I use this option, the FOD becomes very very small and I can't use it for tracking.<br>
<br>
Thank you.<br>
<br>
Regards,<br>
Nyoman<br>
<br>
</div>
</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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