<div dir="ltr"><div>I would like to<a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2014-March/000923.html"> 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 (442) 2 38 10 54<br>Fax (442) 2 38 10 46<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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