Major Fiber Tracts ~~~~~~~~~~~~~~~~~~ .. role:: blue :class: color-blue .. role:: lightblue :class: color-lightblue .. role:: green :class: color-green .. role:: lightgreen :class: color-lightgreen .. role:: orange :class: color-orange .. role:: lightorange :class: color-lightorange .. role:: brown :class: color-brown .. role:: lightbrown :class: color-lightbrown .. role:: pink :class: color-pink .. role:: lightpink :class: color-lightpink .. role:: grey :class: color-grey .. role:: lightgrey :class: color-lightgrey .. role:: teal :class: color-teal .. role:: lightteal :class: color-lightteal .. role:: yellow :class: color-yellow .. role:: lightyellow :class: color-lightyellow .. role:: red :class: color-red .. role:: lightred :class: color-lightred .. role:: gold :class: color-gold .. role:: lightgold :class: color-lightgold .. role:: darkgreen :class: color-darkgreen .. role:: skyblue :class: color-skyblue .. role:: purple :class: color-purple .. role:: darkpurple :class: color-darkpurple .. role:: rose :class: color-rose .. role:: seagreen :class: color-seagreen .. role:: paleyellow :class: color-paleyellow .. role:: darkred :class: color-darkred .. list-table:: List of white matter tracts built-in to pyAFQ :widths: 20 15 20 15 20 :header-rows: 1 :class: long-table * - **Tract Name** - **Color** - **Reference** - **Set** - **Example** * - Left Anterior Thalamic - :blue:`Blue` - :cite:`Yeatman2012` - Default - `Getting started with pyAFQ - GroupAFQ <../tutorials/tutorial_examples/plot_001_group_afq_api.html>`_ * - Right Anterior Thalamic - :lightblue:`Light Blue` - - - * - Left Cingulum Cingulate - :green:`Green` - - - * - Right Cingulum Cingulate - :lightgreen:`Light Green` - - - * - Left Corticospinal - :orange:`Orange` - - - * - Right Corticospinal - :lightorange:`Light Orange` - - - * - Left Inferior Fronto-occipital - :brown:`Brown` - - - * - Right Inferior Fronto-occipital - :lightbrown:`Light Brown` - - - * - Left Inferior Longitudinal - :pink:`Pink` - - - * - Right Inferior Longitudinal - :lightpink:`Light Pink` - - - * - Left Superior Longitudinal - :grey:`Grey` - - - * - Right Superior Longitudinal - :lightgrey:`Light Grey` - - - * - Left Arcuate - :teal:`Teal` - - - * - Right Arcuate - :lightteal:`Light Teal` - - - * - Left Uncinate - :yellow:`Yellow` - - - * - Right Uncinate - :lightyellow:`Light Yellow` - - - * - Left Posterior Arcuate - :red:`Red` - - - * - Right Posterior Arcuate - :lightred:`Light Red` - - - * - Left Vertical Occipital - :gold:`Gold` - - - * - Right Vertical Occipital - :lightgold:`Light Gold` - - - * - Callosum Anterior Frontal - :darkgreen:`Dark Green` - :cite:`Dougherty2007` - - `Callosal bundles using AFQ API <../howto/howto_examples/plot_afq_callosal.html>`_ * - Callosum Motor - :skyblue:`Sky Blue` - - - * - Callosum Occipital - :purple:`Purple` - - - * - Callosum Orbital - :darkpurple:`Dark Purple` - - - * - Callosum Posterior Parietal - :rose:`Rose` - - - * - Callosum Superior Frontal - :seagreen:`Sea Green` - - - * - Callosum Superior Parietal - :paleyellow:`Pale Yellow` - - - * - Callosum Temporal - :darkred:`Dark Red` - - - * - Left Inferior Cerebellar Peduncle - - :cite:`Jossinger2022` - Cerebellar - `Delineating cerebellar peduncles <../howto/howto_examples/cerebellar_peduncles.html>`_ * - Right Inferior Cerebellar Peduncle - - - - * - Left Middle Cerebellar Peduncle - - - - * - Right Middle Cerebellar Peduncle - - - - * - Left Superior Cerebellar Peduncle - - - - * - Right Superior Cerebellar Peduncle - - - - * - Left Acoustic Radiation - - :cite:`Tzourio-Mazoyer2002` - Acoustic Radiations - `Acoustic Radiations Example <../howto/howto_examples/acoustic_radiations.html>`_ * - Right Acoustic Radiation - - - - * - Left Optic Radiation - - :cite:`Caffarra2021` - Optic Radiations - `Optic Radiations Example <../howto/howto_examples/optic_radiations.html>`_ * - Right Optic Radiation - - - - * - Left Superior Longitudinal I - - :cite:`Sagi2024` - Superior Longitudinal Sub-divisions - `SLF 1/2/3 Example <../howto/howto_examples/add_custom_bundle.html>`_ * - Right Superior Longitudinal I - - - - * - Left Superior Longitudinal II - - - - * - Right Superior Longitudinal II - - - - * - Left Superior Longitudinal III - - - - * - Right Superior Longitudinal III - - - - * - Left Optic Tract - - :cite:`Kruper2023` - Posterior Retinogeniculate Visual Pathway - * - Right Optic Tract - - - - * - Left Posterior Optic Nerve - - - - * - Right Posterior Optic Nerve - - - - Custom definitions can also be provided to pyAFQ (see `Defining Custom Bundle Dictionaries `_). The Reference column shows the paper used to create the definitions, and the Set column shows how these are grouped in the software. However, these groups can also be combined and modified.