Brain Modelling

=Infromation sources=
 * Rudolf http://amzn.com/3540346848
 * MAI http://amzn.com/B0084TDIYO
 * FENEIS |http://www.amazon.co.jp/dp/0865779288
 * BREDE WIKI http://neuro.imm.dtu.dk/wiki/Brede_Wiki
 * list of OTHER neuroinfromatics DB: http://neuro.imm.dtu.dk/wiki/Neuroinformatics_database
 * IN RDF : http://www.chibi.ubc.ca/~lfrench/WhiteTextNormalization/SupplementRDF.rdf

=CA-CP line= CA-CP line is originally defined as a line connecting Upper edge of the AC and lower edge of the PC in the mid-sagittal plane.

In our models, some have no clear AC PC contour. So, we used the center of AC PC, that are well-definable, in place of original definition.

In modifying the form of BodyParts data, which is a mosaic of various FORM sources, we assumed AC and PC and the form of cerbral hemisphere are of standard canonicity.

Other parts are modified to be canonical relative to these parts.

=Modeling strategy=

A segmented 3-D living person's MRI model and two cadavour secttion data were used. One of cadavour section data is provided in the form of segmented 3D parts and the other was provided as a a digital atlas of higly segmented and annotated sections. All models have true sizing originally but different position and directions in the model spaces. All model data were converted into obj (polygon) format, enlisting hundereds to thousand edges and vertical vector for every three nodes directing outwards. For every model data, AC was made to (0,0,0) by pararelle shifting and PC was made to (0,Y,0) by the rotation around AC.

Starting from objects close to the AC-PC line, parts were modified from center to peripheri.

i.e.

1. Thalamus: Form 1. antero-posterior size and lateral width were set to xxx and xxx which is reported as average size (ref) 2. meta-thalamus structure sometimes included as thalamus in model were removed along with optic tract. 3. Thalamus form was made similar to SPL brain which has clear internal segmentation. (note SPL thalamus model includes LGB, MGB. They should be removed) 4. Abridging part was set to arbitrary.(small) Position 1. (UP-DOWN) lower edge of the direct contact with thalamus and third ventricluar lining epithelium ( sulcus hypotalamica, lower edge of lateral wall made by the thalamus) was set to be on AC-PC line. (lowest point of thalamus is a bit away from medial plane and a bit lower than this line. 2. (ANT-POST) Thalamus makes anterior 2/3 of upper part of lateral wall of the third ventricle.  Thalamus is a bit behind the mid-AC point.  (Imagine the relation of AC-Fornix-Thalamus)

2. Third ventricle:

Form Triangular form made by connecting  three points ; 1)infundibular recess, 2) PC, 3) AC . Recesses pineal, infundibular, chiasma.  Supra-pineal recess that is a invagination of tela chorioidea is made for the purpose of forming third ventricle as an object.

Position midline section of AC is in the rostral wall of the third ventricle. PC is on the posterior wall of the third ventricle. The roof of the third ventricle is made by tela chorioidea, whose form is flexible. We do not put this roof to the model. (posterior protrusion of this roof corresponds to sura-pineal recess) The stria medullaris on the dorsal surface of the thalamus is shown as a attachement line of this flexible roof to the ridgid structure.

3. Additional structure on the lower and posterior wall of the third ventricle. Mammilary body Pineal body AC, PC    Pituitary stalk LGB-optic tract-optic chiasma-optic nerve

3. Roof structures Fornix : collumn of the fornix at the rostral edge of the thalamus. Lateral Foramen behid fornix collumn and thalamus. Mind Direct adhesion to fornix and corpus callosum in the body of fornix in the middle line and posteriorly laterally. Corpus callosum: Septum pellusidum Lateral ventricles:

Mind: what is making the anterior wal of the lateral ventricle./ Corpus callosum--genu of cc-- Anterior commssure+Fornix-- lamina terminalis--vhiasma opticus--infundiburum

1. Shape of the Thalamus (excluding meta-thalamus i.e. LGB, MGB)

Dimensitions antero-posterior right-left top-bottom

Three models and literature

Adjust the size and shape of thalamus.

2. Position of thalamus making third and fource ventricle

Adjust the antero-posterior position relative to distance from AC Adjust the up-down position relative to ac-pc line Hypothalamic sulcus on the lateral wall of the third ventricle is on the AC-PC line (Gray)

Internal surface connected bilaterally with

3. Overlay the caudate nucleus (leave the head shape as it is) to thalamus

Shape of caudate nucleus

Head shape: Caudate nucleus is

Mind the direct contact between thalamus and caudate border between thalamus and caudate body on the internal surcface of lateral ventricle is called sulcus terminalis which is covered by "stria terminalis." Stria terminalis is a nerve fiber ends in amygdala.