Todd<br><br>Thanks for sending those images; it makes the discussion a whole lot more clear.<br><br>Firstly, I don't see anything fundamentally 'wrong' with your images; your processing appears to be fine.<br>I would however like to discuss a few points with regards to the observations you have made, for anyone interested enough to continue reading:<br>
<br><br>* Although you haven't provided an example image, you noted that the discrepancy between the TDI and anatomical image appears most prominent in the genu of the corpus callosum.<br> Most likely this is caused by susceptibility-induced geometric distortions. For a standard EPI acquisition with the phase-encode direction running anterior-posterior, the genu is shifted posteriorly by as much as a couple of voxels; it's not enough to make the DWIs look 'wrong' when viewed independently, but it's highly noticeable when you overlay them on a non-EPI image.<br>
In my experience, the best results for susceptibility distortion correction (in terms of both acquisition time and accuracy) are obtained using the reversed-phase-encode method (<a href="http://www.sciencedirect.com/science/article/pii/S1053811909012294">this</a><a> method</a> is probably easiest to read and understand). Our lab now acquires a reversed-phase-encode b=0 pair for this purpose, for every subject scanned. I had done some experimentation with methods for estimating the inhomogeneity field from such an image pair, in the hope of including something in MRtrix, but the tools included in FSL5 ('topup' and 'applytopup') work better than anything I've come up with thus far. You do NOT need to acquire a reversed phase-encode image for every single DW direction (although it can yield better results); a single echo-planar image pair is enough to estimate the inhomogeneity field and 'shift' the DW signal back to its correct spatial position.<br>
<br>* The overlap between the TDI and the ventricles is commonplace, and occurs due to a combination of factors.<br> The default FOD amplitude threshold for streamline termination is 0.1; maximal FOD values are around 3.0. Now imagine a voxel that is half corpus callosum, half ventricle, that has an FOD peak amplitude of 1.5, and the voxel adjacent to it is in the ventricle and has zero FOD amplitude. As the streamlines algorithm interpolates the FODs as it tracks, streamlines can go almost all the way out to the centre of the ventricle voxel before the (interpolated) FOD amplitude threshold is disobeyed; this is why the tracking algorithm substantially over-estimates the cross-section of the corpus callosum (clearer when viewed on a mid-sagittal slice of the T1 / TDI).<br>
Correction of reconstruction errors such as this are the target of my <a href="http://www.sciencedirect.com/science/article/pii/S1053811912005824">Anatomically-Constrained Tractography</a> framework, which makes use of a segmented T1 image during the tracking process. Streamlines entering the ventricles are not only terminated, but rejected entirely (as we don't expect white matter connections to enter the ventricles). This will be included in the next major release of MRtrix; but it relies on very good correspondence between the DWIs and the T1, which is why I recommend acquisition of reversed-phase-encode image pairs as soon as possible (so you can use this capability on retrospective data).<br>
<br>* The final issue you raise is the contrast present in the TDIs, where the intensity is highest in the corpus callosum (particularly its inferior edge) and doesn't necessarily match the FA map.<br> This is not surprising at all, as the two images draw their contrast from very different sources. Neither the streamline density nor the FA are accurate markers of 'white matter connection density' (<a href="http://www.sciencedirect.com/science/article/pii/S1053811912007306">this paper</a> by Derek Jones is worth a read), so care needs to be taken in the interpretation of both sources.<br>
But since I've already strayed down the path of self-proclamation, I might as well mention my recently-published <a href="http://www.sciencedirect.com/science/article/pii/S1053811912011615">SIFT</a> method. This tries to match the streamline densities with the tissue volumes estimated by CSD; as a result, the TDIs look very much like the DC term of the relevant FOD image. To me this is a much better quantification of 'white matter connection density' than FA, TDI, or the <i>ad hoc</i> metrics being used by the connectomics community. So I'm looking forward to seeing what people do with it when it's released.<br>
<br><br><br>Anyway, I hope that was all at least somewhat interesting / informative for yourself or others out there in the ęther...<br><br>Rob<br clear="all"><div class="gmail_extra"><div><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></div>
<br><br><div class="gmail_quote">On Sat, Jan 5, 2013 at 7:31 PM, Todd Jolly <span dir="ltr"><<a href="mailto:todd.jolly@uon.edu.au" target="_blank">todd.jolly@uon.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi Rob,<br>
No problem, I have attached a couple of images to show you what I mean. These show the TDI overlayed on the FA map.<br>
Thanks<br>
Todd<br>
<div style="font-size:16px;font-family:Times New Roman">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Robert Smith [<a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a>]<br>
<b>Sent:</b> Saturday, 5 January 2013 2:13 PM<br>
<b>To:</b> Todd Jolly<br>
<b>Subject:</b> Re: [Mrtrix-discussion] TDI map differs from FA map<br>
</font><br>
</div><div><div class="h5">
<div></div>
<div>
<div>Todd<br>
</div>
<div><br>
</div>
<div>Could you forward me a couple of example images to demonstrate exactly what you mean? It's difficult to establish what the problem may be from your description alone.</div>
<div><br>
</div>
<div>Rob</div>
<div class="gmail_extra"><br clear="all">
<div><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: <a href="tel:%2B61%203%209035%207128" value="+61390357128" target="_blank">+61 3 9035 7128</a><br>
Fax: <a href="tel:%2B61%203%209035%207301" value="+61390357301" target="_blank">+61 3 9035 7301</a><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></div>
<br>
<br>
<div class="gmail_quote">On Sat, Jan 5, 2013 at 1:57 PM, Todd Jolly <span dir="ltr">
<<a href="mailto:todd.jolly@uon.edu.au" target="_blank">todd.jolly@uon.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi everyone,<br>
I have been performing whole-brain tracking and using this to generate track density images. I have noticed that the track density images differ from my anatomical or FA images. The TDI appear to be including regions that the anatomical images are classifying
as being the lateral ventricle. This is most noticeable for the genu of the corpus callosum.<br>
I am concerned as these regions that are classified as CSF in the anatomical and FA images appear have the highest track density in the TDI? Is this normal for there to be a discrepancy or have I made an error somewhere in the processing of these data?<br>
Thanks in advance<span><font color="#888888"><br>
Todd<br>
</font></span></div>
</div>
<br>
_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">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>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div></div></div>
</div>
</div>
</blockquote></div><br></div>