[Mrtrix-discussion] AFD per fixel

[Luis Concha]

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/
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