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[DOC] Describe mrtrix connectivity matrix outputs #689

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[DOC] Describe mrtrix connectivity matrix outputs #689

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21 changes: 21 additions & 0 deletions docs/reconstruction.rst
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Expand Up @@ -250,6 +250,27 @@ Pre-configured recon_workflows
were calculated using SIFT2_ [Smith2015]_ and were included for while estimating the
structural connectivity matrix.

The MRtrix workflows generate a variety of outputs. These include:

* WM FOD, GM-like, and CSF-like compartment files. Both original (wmFOD, gmFOD, csfFOD .mif.gz
files) and bias field corrected/intensity normalized (wmFODmtnormed, gmFODmtnormed,
csfFODmtnormed .mif.gz files) files are written. These are the outputs of dwi2fod and
mtnormalise, respectively
* atlas files of interest in .mig.gz and .nii.gz formats, with corresponding txt files
* a .mat file, which contains cortico-cortical and cortical-subcortical structural connectivity
matrices for numerous atlases. This mat file contains information about regional
numbers/labels for each atlas as well as 4 structural connectome outputs for each atlas.
The 4 connectivity matrix outputs are
*radius#.count.connectivity*: raw streamline count based matrix
*sift.radius#.count.connectivity*: sift-weighted streamline count based matrix
*radius#.meanlength.connectivity*: a matrix containing mean length of raw streamlines
*sift.radius#.meanlenght.connectivity*: a matrix containing mean length of sifted output

The number # in radius# indicates how many mm the algorithm would search up from a
given streamline's endpoint for a cortical region. E.g., a radius of 2 indicates that
if a streamline ended before hitting gray matter, the search for a cortical
termination region could be up to 2mm from the endpoint.


.. warning::
We don't recommend using ACT with FAST segmentations. The full benefits of ACT
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