<div dir="ltr">Hi Luis,<div><br></div><div>One thing I probably should include in the documentation is that the AFD in this command is actually computed as the FOD fixel <i>integral</i> (as explained in Rob's SIFT paper). The afdconnectivity command parses each streamline, and identifies which fixels are tangent to the streamline. After all fixels have been identified it <i>sums</i> the AFD (integral) over all fixels, then normalises by mean streamline length. <br>
</div><div><br></div><div>To answer your questions:<br></div><div><br></div><div>a) Yes afdconnectivity will only include fixels that are tangent to your streamlines and will ignore fixels from unrelated crossing fibres. There is no angular threshold for assigning fixels to the streamline tangent. If a streamline passes through a voxel, then the fixel with the closest orientation to the streamline tangent will be flagged as belonging to the tract. Assuming you have used the same FOD image for tractography and AFD calculations then this should not be an issue. </div>
<div><br></div><div>b) If the streamlines are neatly aligned then only a single fixel will be included. However sometimes with probabilistic tracking they branch off in different directions in crossing fibre regions. In this case multiple fixels within a single voxel may be flagged as belonging to the tract-of-interest. Note we don't just sum the AFD within a voxel, the afdconnectivity measure is the sum of AFD from <i>all</i> fixels in the tract of interest. This is then normalised by mean streamline length to get a measure related to fibre <i>bundle</i> cross-sectional area. If we were to average the AFD then morphological differences in fibre bundle width will not contribute to the connectivity of a bundle. We normalise by mean streamline length since subject differences in fibre bundle <i>length</i> are unlikely to influence "connectivity". </div>
<div><br></div><div>c) I'm not entirely sure how the tckmap AFD stuff is implemented. Rob can you comment on this one?<br></div><div><br></div><div>d) afdconnectivity inputs the FOD image, segments the fixels and computes the AFD integral for you (you need to input the FOD image, not a AFD fixel image). Although I admit inputting a fixel image makes more sense, however afdconnectivity was coded before we had the mtrix sparse image format. We should probably change this in the future. </div>
<div><br></div><div>Just a final comment. I coded afdconnectivity as a fairly adhoc method of computing tract-of-interest AFD for situations where ACT and SIFT could not be used. If you have EPI correction, then a more robust AFD-based connectivity measure would be to do whole brain tracking, SIFT, then count the streamlines between your regions of interest.</div>
<div><br></div><div>Cheers,</div><div>Dave</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br><div class="gmail_extra"><br><br><div class="gmail_quote">On 27 June 2014 09:04, Luis Concha <span dir="ltr"><<a href="mailto:lconcha@unam.mx" target="_blank">lconcha@unam.mx</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div>I would like to<a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2014-March/000923.html" target="_blank"> revisit the topic</a> of tract-specific AFD measurements in light of the new and useful tools available in mrtrix3.</div>
<div><br></div><div>Looking at the documentation of afdconnectivity, the option -afd otuputs a volume containing the AFD estimated for each voxel, given a track file. However, it clearly states that "if the input tracks are tangent to multiple fibres in a voxel(fixels), then the output AFD is the sum of the AFD for each fixel". I am a bit confused by this statement and have a few questions:</div>
<div><br></div><div>a) Imagine a streamline belonging to the corpus callosum passing through the centrum semiovale; I would like to obtain the AFD from the fixels most parallel to the streamline segment, and ignore the other (presumably perpendicular) fixel. Does afdconnectivity do this? And, if so, how "perpendicular" does the fixel orientation need to be relative to the track segment in order to be included?</div>
<div><br></div><div>b) Now imagine several tracks passing through the same voxel, all of them neatly parallel with the fixel orientation. Why would we want to obtain the sum of AFDs, as opposed to the average AFD in that voxel? The choice to sum seems susceptible by the number of tracks generated and thus passing through the voxel in questionq. </div>
<div><br></div><div>c) From the documentation for tckmap it seems like I can have the mean instead of the sum by way of the -stat_vox mean switch. However, in this command I am not clear if fixels are selected in terms of perpendicularity to the track segment or not (it seems unlikely, as the FODs are not segmented, but rather the average -or sum- of all the AFDs in a given voxel). </div>
<div><br></div><div>d) Finally, I am getting an error when using afdconnectivity:</div><div><div>$ afdconnectivity -afd callosum_afd.nii fixel_afd.msf callosum.tck -info</div><div>afdconnectivity </div><div>[INFO]: opening image "fixel_afd.msf"...</div>
<div>afdconnectivity: summing apparent fibre density within track... 0%afdconnectivity [INFO]: opening image "fixel_afd.msf"...</div><div>afdconnectivity [INFO]: opening image "fixel_afd.msf"...</div>
<div>afdconnectivity: summing apparent fibre density within track... 2%Segmentation fault (core dumped)</div></div><div><br clear="all"><div><div>(the same error occurs even if -afd is not used).</div><div><br></div><div>
<br></div><div>I apologize for so many questions in a single post, but they are all related.Thanks in advance. </div><div dir="ltr"><br></div><div dir="ltr"><br></div><div>FYI:</div><div><div>$ afdconnectivity -version</div>
<div>== afdconnectivity 6d02b643 ==</div><div>64 bit release version, built May 29 2014, using GSL 1.16</div></div><div><br></div><div dir="ltr"><div dir="ltr">************************************************</div><div dir="ltr">
Image: "fixel_afd.msf"</div><div dir="ltr">************************************************</div><div dir="ltr"> Format: MRtrix WIP sparse image data format</div><div dir="ltr"> Dimensions: 256 x 256 x 54</div>
<div dir="ltr"> Voxel size: 1 x 1 x 2</div><div dir="ltr"> Data type: unsigned 64 bit integer (little endian)</div><div dir="ltr"> Data strides: [ 2 3 1 ]</div><div dir="ltr"> Intensity scaling: offset = 0, multiplier = 1</div>
<div dir="ltr"> Comments: FSL4.1</div><div dir="ltr"> Properties:</div><div dir="ltr"> sparse_data_name: N2MR5Image6Sparse11FixelMetricE</div><div dir="ltr"> sparse_data_size: 20</div><div dir="ltr"> Transform: 1 0 0 -127.7</div>
<div dir="ltr"> -0 1 0 -111.5</div><div dir="ltr"> -0 0 1 -49.73</div><div dir="ltr"> 0 0 0 1</div>
<div><div>***********************************</div><div> Tracks file: "callosum.tck"</div><div> count: 50</div><div> downsample_factor: 3</div><div> fod_power: 0.25</div><div>
init_threshold: 0.1</div><div> lmax: 8</div></div><div><br></div></div><div dir="ltr"><br></div><div dir="ltr"><div dir="ltr">$ uname -a</div><div dir="ltr">Linux mansfield 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux</div>
<div><br></div></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">Dr. Luis Concha<br>Instituto de Neurobiología<br>Laboratorio C-13<br>UNAM, Campus Juriquilla<br>Boulervard Juriquilla 3001<br>Juriquilla, Querétaro.<br>
C.P. 76230<br>México<br>Tel <a href="tel:%28442%29%202%2038%2010%2054" value="+14422381054" target="_blank">(442) 2 38 10 54</a><br>Fax <a href="tel:%28442%29%202%2038%2010%2046" value="+14422381046" target="_blank">(442) 2 38 10 46</a><br>
<a href="http://personal.inb.unam.mx/lconcha/" target="_blank">http://personal.inb.unam.mx/lconcha/</a><br></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div><b><font color="#ff6600">David Raffelt (PhD)</font></b></div><div><font color="#ff6600">Post Doctoral Fellow</font></div><div><br></div>
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