[Mrtrix-discussion] AFD per fixel
David Raffelt
d.raffelt at brain.org.au
Thu Jun 26 17:09:00 PDT 2014
Hi Luis,
One thing I probably should include in the documentation is that the AFD in
this command is actually computed as the FOD fixel *integral* (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 *sums* the AFD (integral) over all fixels, then
normalises by mean streamline length.
To answer your questions:
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.
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 *all* fixels in the tract of
interest. This is then normalised by mean streamline length to get a
measure related to fibre *bundle* 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 *length* are
unlikely to influence "connectivity".
c) I'm not entirely sure how the tckmap AFD stuff is implemented. Rob can
you comment on this one?
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.
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.
Cheers,
Dave
On 27 June 2014 09:04, Luis Concha <lconcha at unam.mx> wrote:
> I would like to revisit the topic
> <http://www.nitrc.org/pipermail/mrtrix-discussion/2014-March/000923.html>
> of tract-specific AFD measurements in light of the new and useful tools
> available in mrtrix3.
>
> 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:
>
> 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?
>
> 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.
>
> 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).
>
> d) Finally, I am getting an error when using afdconnectivity:
> $ afdconnectivity -afd callosum_afd.nii fixel_afd.msf callosum.tck -info
> afdconnectivity
> [INFO]: opening image "fixel_afd.msf"...
> afdconnectivity: summing apparent fibre density within track...
> 0%afdconnectivity [INFO]: opening image "fixel_afd.msf"...
> afdconnectivity [INFO]: opening image "fixel_afd.msf"...
> afdconnectivity: summing apparent fibre density within track...
> 2%Segmentation fault (core dumped)
>
> (the same error occurs even if -afd is not used).
>
>
> I apologize for so many questions in a single post, but they are all
> related.Thanks in advance.
>
>
> FYI:
> $ afdconnectivity -version
> == afdconnectivity 6d02b643 ==
> 64 bit release version, built May 29 2014, using GSL 1.16
>
> ************************************************
> Image: "fixel_afd.msf"
> ************************************************
> Format: MRtrix WIP sparse image data format
> Dimensions: 256 x 256 x 54
> Voxel size: 1 x 1 x 2
> Data type: unsigned 64 bit integer (little endian)
> Data strides: [ 2 3 1 ]
> Intensity scaling: offset = 0, multiplier = 1
> Comments: FSL4.1
> Properties:
> sparse_data_name: N2MR5Image6Sparse11FixelMetricE
> sparse_data_size: 20
> Transform: 1 0 0 -127.7
> -0 1 0 -111.5
> -0 0 1 -49.73
> 0 0 0 1
> ***********************************
> Tracks file: "callosum.tck"
> count: 50
> downsample_factor: 3
> fod_power: 0.25
> init_threshold: 0.1
> lmax: 8
>
>
> $ uname -a
> 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
>
>
>
> Dr. Luis Concha
> Instituto de Neurobiología
> Laboratorio C-13
> UNAM, Campus Juriquilla
> Boulervard Juriquilla 3001
> Juriquilla, Querétaro.
> C.P. 76230
> México
> Tel (442) 2 38 10 54
> Fax (442) 2 38 10 46
> http://personal.inb.unam.mx/lconcha/
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>
--
*David Raffelt (PhD)*
Post Doctoral Fellow
The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7024
www.florey.edu.au
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