Hi Dan<br><br>Regarding the interpretation of Fibre Orientation
Distribution amplitudes, I would suggest looking at the diffusion
simulations in:<br>Raffelt, D., Tournier, J-D., Rose, S., Ridgway, G.R., Henderson, R., Crozier, S., Salvado, O., Connelly, A.. Apparent Fibre Density: A novel measure for the analysis of diffusion-weighted magnetic resonance images. NeuroImage 2012:59;3976-3994.<br>
<br>For high <i>b</i>-value acquisitions, and assuming that you do <u>not</u> normalise to the <i>b=0</i> signal (which we recommend, and occurs by default), the amplitude of the FOD is approximately proportional to the <i>intra-cellular volume</i> of axons aligned in that particular orientation. The FOD peak amplitudes are then a reasonable sparse representation of this, so you can estimate the relative volume of axons in a voxel in different orientations. Note however that I said <i>volume</i> of axons rather then <i>number</i>; a single high <i>b</i>-value acquisition is more or less insensitive to axon diameter, so we can't distinguish between many small-diameter axons and fewer large-diameter axons, because the total intra-cellular volume is more or less the same.<br>
<br>The FOD peak amplitudes are however not the ideal marker, as orientation dispersion can introduce 'spread' into the FOD lobe and reduce the peak amplitude. I have developed a method that instead computes the integral of individual FOD lobes, which is more robust against these effects; the details should be included in a publication later this year.<br>
<br>Best regards<br>Rob<br clear="all"><br>--<br><br>Robert Smith<br>PhD Candidate <br><br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>245 Burgundy Street<br>Heidelberg Vic 3084<br>
Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span><br>
<br><br><div class="gmail_quote">On Tue, Sep 11, 2012 at 3:20 AM, Dan Wu <span dir="ltr"><<a href="mailto:dwu18@jhu.edu" target="_blank">dwu18@jhu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear expert,<div><br></div><div>I used the find_SH_peaks to get the peak directions of the FODs. I am wondering what the magnitude of the peak FOD represents? Does it relates to the diffusion signal along that direction or it is just a relative magnitude?</div>
<div><br></div><div>Thanks a lot!</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Dan<br><br clear="all"><div><br></div>-- <br>Dan Wu<br><br>PhD Candidate<br>Department of Biomedical Engineering<br>Johns Hopkins University<br>
email: <a href="mailto:dwu18@jhu.edu" target="_blank">dwu18@jhu.edu</a><br>
phone: <a href="tel:443-564-9191" value="+14435649191" target="_blank">443-564-9191</a><br><br>
</div>
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