Editing Tractography (section)

== MRI technique ==
{{Unreferenced section|date=September 2018}}
[[File:Deterministic Tractography of the Adult Brachial Plexus using Diffusion Tensor Imaging.gif|thumb|DTI of the brachial plexus - see https://doi.org/10.3389/fsurg.2020.00019 for more information]]
<!-- Image with unknown copyright status removed: [[Image:Fallon_Petrovic_DTI_lat3.jpg|right|Image of a streamlined DTI scan of the whole human brain seen from the side: Fallon&Petrovic UC Irvine]] -->
[[Image:DTI-sagittal-fibers.jpg|thumb|240px|Tractographic reconstruction of neural connections by diffusion tensor imaging (DTI)]]
[[File:Ultra-High-Field-MRI-Post-Mortem-Structural-Connectivity-of-the-Human-Subthalamic-Nucleus-Video1.ogv|thumb|240px|MRI tractography of the human [[subthalamic nucleus]]]]
Tractography is performed using data from [[diffusion MRI]]. The free water diffusion is termed "[[isotropic]]" diffusion. If the water diffuses in a medium with barriers, the diffusion will be uneven, which is termed [[anisotropic]] diffusion. In such a case, the relative mobility of the [[molecules]] from the origin has a shape different from a [[sphere]]. This shape is often modeled as an [[ellipsoid]], and the technique is then called [[diffusion tensor imaging]].<ref>{{cite journal | vauthors = Basser PJ, Mattiello J, LeBihan D | title = MR diffusion tensor spectroscopy and imaging | journal = Biophysical Journal | volume = 66 | issue = 1 | pages = 259–267 | date = January 1994 | pmid = 8130344 | pmc = 1275686 | doi = 10.1016/S0006-3495(94)80775-1 | bibcode = 1994BpJ....66..259B }}</ref> Barriers can be many things: cell membranes, axons, myelin, etc.; but in [[white matter]] the principal barrier is the [[myelin]] sheath of [[axons]]. Bundles of axons provide a barrier to perpendicular diffusion and a path for parallel diffusion along the orientation of the fibers.

Anisotropic diffusion is expected to be increased in areas of high mature axonal order. Conditions where the [[myelin]] or the structure of the axon are disrupted, such as [[Physical trauma|trauma]],<ref>{{cite journal | vauthors = Wade RG, Tanner SF, Teh I, Ridgway JP, Shelley D, Chaka B, Rankine JJ, Andersson G, Wiberg M, Bourke G | title = Diffusion Tensor Imaging for Diagnosing Root Avulsions in Traumatic Adult Brachial Plexus Injuries: A Proof-of-Concept Study | journal = Frontiers in Surgery | volume = 7 | pages = 19 | date = 16 April 2020 | pmid = 32373625 | pmc = 7177010 | doi = 10.3389/fsurg.2020.00019 | doi-access = free }}</ref> [[tumors]], and [[inflammation]] reduce anisotropy, as the barriers are affected by destruction or disorganization.

Anisotropy is measured in several ways. One way is by a ratio called [[fractional anisotropy]] (FA). An FA of 0 corresponds to a perfect sphere, whereas 1 is an ideal linear diffusion. Few regions have FA larger than 0.90. The number gives information about how aspherical the diffusion is but says nothing of the direction.

Each anisotropy is linked to an orientation of the predominant axis (predominant direction of the diffusion). Post-processing programs are able to extract this directional information.

This additional information is difficult to represent on 2D grey-scaled images. To overcome this problem, a color code is introduced. Basic colors can tell the observer how the fibers are oriented in a 3D coordinate system, this is termed an "anisotropic map". The software could encode the colors in this way:
* Red indicates directions in the ''X'' axis: right to left or left to right.
* Green indicates directions in the ''Y'' axis: [[Posterior (anatomy)|posterior]] to anterior or from [[anterior]] to posterior.
* Blue indicates directions in the ''Z'' axis: [[Anatomical terms of location|inferior]] to [[Anatomical terms of location|superior]] or vice versa.

The technique is unable to discriminate the "positive" or "negative" direction in the same axis.