Standardized in QMRITools

Muscle segmentation naming

A generalized muscle naming convention

A canonical numeric ID and data format for muscles, bones, and groups. It is designed to work as a translation layer: any lab, tool, or piece of software can map its own local label numbers to these canonical IDs, and translate between systems through them.

The format is a plain data file (JSON), readable by any language or tool. This document describes the ID scheme and record structure.

ID scheme

Every entry has one integer ID:

id = region * 1000 + index * 10 + side

region (1 digit)

The body part the entry belongs to. Nine slots, all currently in use:

#region
1Head
2Neck
3Shoulder
4Arm
5Thorax
6Hip
7Thigh
8Leg
9Bones

index (2 digits)

Position within the region, split by type:

rangemeaning
01–69a muscle
70–99a group

side (1 digit)

valuemeaning
0none — no left/right distinction (midline structures)
1left
2right
3both — one entry covering left and right together

type: muscle vs. bone vs. group

Every entry is "muscle", "bone", or "group", and this always matches the index range: "muscle" and "bone" entries always have an index in 01–69, a "group" always has an index in 50–99. This is a fixed rule — checking that an entry’s type matches its index range is a basic validity check on the data.

  • muscle — one anatomical muscle. It may still have children: a muscle that is described as having “heads” or “parts” (e.g. Biceps Brachii has a long and short head) is one "muscle" entry whose children are also "muscle" entries.
  • bone — one anatomical bone, used only in the Bones region. Like muscle, a bone may have children if it is described as having distinct named parts.
  • group — a set of separate entries bundled together by compartment, function, or region (e.g. Rotator Cuff, Quadriceps, or a compartment like “Deep Posterior Compartment”). Groups can contain muscles, bones, other groups, or a mix of these, and can be nested arbitrarily deep — a compartment containing a sub-compartment containing a functional group is just three "group" entries, one inside the next.

Whether an entry is a leaf (nothing further underneath it) is a separate question from type, and is answered by whether its children list is empty — not by type. A leaf muscle (no children) and a muscle with heads (has children) are both type: "muscle"; the same applies to bones.

Parent / compartment lookup

An entry does not store which group(s) it belongs to. That is always found by searching: to find what an entry is part of, look through every "group" entry’s children list for that entry’s ID. This keeps the tree one-directional — parents list their children, children never list their parents — so there is only one place that can go out of sync.

Left / right / both

A paired structure gets three entries sharing the same region and index, differing only in the side digit — for example a muscle at index 14 in region 7:

7141 -> left
7142 -> right
7143 -> both

A structure with no left/right distinction (e.g. a midline bone or a midline muscle) gets exactly one entry, with side 0.

Example: a muscle and a group, both exploded by side

A single muscle, e.g. Semitendinosus in the Thigh region (region 7, index 04), becomes three entries:

7041 -> semitendinosus (left)
7042 -> semitendinosus (right)
7043 -> semitendinosus (both)

A group is exploded the same way if the thing it represents is itself a paired, bilateral structure. Vastus (region 7, index 60, a group of Vastus Lateralis / Intermedius / Medialis) also becomes three entries — one per side — and each side’s group points only to the matching side of its children:

7601 -> vastus (left)  -> children: [vastus lateralis (left), vastus intermedius (left), vastus medialis (left)]
7602 -> vastus (right) -> children: [vastus lateralis (right), vastus intermedius (right), vastus medialis (right)]
7603 -> vastus (both)  -> children: [vastus lateralis (both), vastus intermedius (both), vastus medialis (both)]

A left-side group never mixes in a right-side child, and vice versa — each side of a group is a self-contained tree of that same side, all the way down.

children vs. side — two separate axes

children only ever expresses composition — what an entry is made of, or what a group contains. It never expresses sidedness. semitendinosus (both) does not list semitendinosus (left) and semitendinosus (right) as its children, and a group’s left entry does not list its right entry as a child either.

Same-side and other-side siblings are never found by searching — they are computed directly from the id, by changing only the side digit:

7043 (both) -> swap side digit -> 7041 (left), 7042 (right)

This keeps the two relationships independent: walking children answers “what does this contain,” and reading/changing the side digit answers “which side is this.” Neither one is a substitute for the other, and nothing about side is ever discovered by traversing children.

Record format

fielddescription
idcanonical integer, per the scheme above
namecanonical name
type"muscle", "bone", or "group"
regionone of the nine regions above
side"none", "left", "right", or "both"
childrenlist of child IDs. Empty for leaves.
color[R, G, B]
aliaslist of alternate names or spellings for this entry
abbreviationabbreviated name of the muscle of group

Example:

{
  "id": 4013,
  "name": "biceps brachii",
  "type": "muscle",
  "region": "arm",
  "side": "both",
  "children": [4023, 4033],
  "color": [157, 54, 13],
  "alias": [],
  "abbreviation": []
}

with its two heads as their own entries:

{
  "id": 4023,
  "name": "long head of biceps brachii",
  "type": "muscle",
  "region": "arm",
  "side": "both",
  "children": [],
  "color": [168, 70, 30],
  "alias": [],
  "abbreviation": []
}

Muscle Lookup

Bold items are groups, plain items are individual muscles or bones. (midline) marks anything with no left/right distinction (side: none in the JSON) — everything else is paired and gets left/right/both entries.

1. Head

  • Tongue
    • Intrinsic
      • Inferior Longitudinal Of Tongue
      • Superior Longitudinal Of Tongue
      • Transverse Of Tongue
      • Vertical Of Tongue
    • Extrinsic
      • Genioglossus
      • Hyoglossus
      • Styloglossus
      • Palatoglossus
  • Facial Orbital Compartment
    • Orbicularis Oculi
    • Corrugator Supercilii
  • Facial Nasal Compartment
    • Nasalis
    • Procerus (midline)
    • Depressor Septi Nasi
  • Facial Oral Compartment
    • Orbicularis Oris (midline)
    • Buccinator
  • Mastication Compartment
    • Masseter
    • Temporalis
    • Medial Pterygoid
    • Lateral Pterygoid

2. Neck

  • Suboccipital Compartment
    • Rectus Capitis Posterior Major
    • Rectus Capitis Posterior Minor
    • Obliquus Capitis Inferior
    • Obliquus Capitis Superior
  • Suprahyoids Compartment
    • Stylohyoid
    • Digastric
    • Mylohyoid
    • Geniohyoid
  • Infrahyoids Compartment
    • Omohyoid
    • Sternohyoid
    • Sternothyroid
    • Thyrohyoid
  • Scalenes Compartment
    • Scalenus Anterior
    • Scalenus Medius
    • Scalenus Posterior
  • Prevertebral Muscles
    • Longus Colli
    • Longus Capitis
    • Rectus Capitis Anterior
    • Rectus Capitis Lateralis
  • Sternocleidomastoid
  • Splenius
    • Splenius Capitis
    • Splenius Cervicis

3. Shoulder

  • Posterior Extrinsic Compartment of the Shoulder
    • Trapezius
    • Latissimus Dorsi
    • Levator Scapulae
    • Rhomboids
      • Rhomboid Minor
      • Rhomboid Major
  • Rotator Cuff
    • Supraspinatus
    • Infraspinatus
    • Subscapularis
    • Teres Minor
  • Posterior Intrinsic Compartment of the Shoulder
    • Deltoid
      • Clavicular Part Of Deltoid
      • Acromial Part Of Deltoid
      • Scapular Part Of Deltoid
    • Teres Major
  • Anterior Compartment of the Shoulder
    • Pectoralis Major
      • Abdominal Part Of Pectoralis Major
      • Sternocostal Part Of Pectoralis Major
      • Clavicular Part Of Pectoralis Major
    • Pectoralis Minor
    • Serratus Anterior
    • Subclavius

4. Arm

  • UpperArm
    • Anterior Compartment of the Upper Arm
      • Biceps Brachii
        • Long Head Of Biceps Brachii
        • Short Head Of Biceps Brachii
      • Coracobrachialis
      • Brachialis
    • Posterior Compartment of the Upper Arm
      • Triceps Brachii
        • Lateral Head Of Triceps Brachii
        • Medial Head Of Triceps Brachii
        • Long Head Of Triceps Brachii
  • Forearm
    • Anterior Superficial Compartment of the Forearm
      • Flexor Carpi Ulnaris
        • Ulnar Head Of Flexor Carpi Ulnaris
        • Humeral Head Of Flexor Carpi Ulnaris
      • Palmaris Longus
      • Flexor Carpi Radialis
      • Pronator Teres
      • Flexor Digitorum Superficialis
        • Radial Head Of Flexor Digitorum Superficialis
        • Humeroulnar Head Of Flexor Digitorum Superficialis
    • Anterior Deep Compartment of the Forearm
      • Flexor Pollicis Longus
      • Flexor Digitorum Profundus
      • Pronator Quadratus
    • Posterior Superficial Compartment of the Forearm
      • Brachioradialis
      • Extensor Carpi Radialis
        • Extensor Carpi Radialis Brevis
        • Extensor Carpi Radialis Longus
      • Extensor Digitorum
      • Extensor Carpi Ulnaris
      • Extensor Digiti Minimi
      • Anconeus
    • Posterior Deep Compartment of the Forearm
      • Supinator
      • Abductor Pollicis Longus
      • Extensor Pollicis Brevis
      • Extensor Pollicis Longus
      • Extensor Indicis

5. Thorax

  • Back
    • Intermediate Compartment of the Back
      • Serratus Posterior Superior
      • Serratus Posterior Inferior
    • Erector Spinae Compartment
      • Iliocostalis
      • Longissimus
      • Spinalis
    • Deep Intrinsic Compartment of the Back
      • Transversospinales Group
        • Semispinalis
        • Multifidus
        • Rotator
      • Minor Deep Intrinsic
        • Interspinalis
        • Intertransversarii
        • Levatores Costarum
  • Abdomen
    • Anterolateral Compartment of the Abdomen
      • External Oblique
      • Internal Oblique
      • Transversus Abdominis
      • Rectus Abdominis
      • Pyramidalis
    • Posterior Compartment of the Abdomen
      • Quadratus Lumborum
      • Diaphragm (midline)
  • Chest
    • Intercostal muscles
      • External intercostals
      • Internal intercostals
      • Innermost intercostals

6. Hip

  • Anterior Compartment of the Hip
    • Iliopsoas
      • Iliacus
      • Psoas Major
  • Superficial Compartment of the Hip
    • Gluteus
      • Gluteus Maximus
      • Gluteus Medius
      • Gluteus Minimus
    • Tensor Fasciae Latae
  • Deep Compartment of the Hip
    • Piriformis
    • Obturator Internus
    • Obturator Externus
    • Gemelli
      • Gemellus Superior
      • Gemellus Inferior
    • Quadratus Femoris
  • Pelvis Compartment
    • Levator Ani
      • Puborectalis
      • Pubococcygeus
      • Iliococcygeus
    • Coccygeus

7. Thigh

  • Posterior Compartment of the Thigh
    • Biceps Femoris
      • Long Head Of Biceps Femoris
      • Short Head Of Biceps Femoris
    • Semimembranosus
    • Semitendinosus
  • Medial Compartment of the Thigh
    • Adductor
      • Adductor Magnus
      • Adductor Minimus
      • Adductor Longus
      • Adductor Brevis
    • Gracilis
    • Pectineus
  • Anterior Compartment of the Thigh
    • Quadriceps Femoris
      • Vastus
        • Vastus Lateralis
        • Vastus Intermedius
        • Vastus Medialis
      • Rectus Femoris
    • Sartorius

8. Leg

  • Superficial Posterior Compartment of the Leg
    • Gastrocnemius
      • Lateral Head Of Gastrocnemius
      • Medial Head Of Gastrocnemius
    • Soleus
    • Plantaris
  • Deep Posterior Compartment of the Leg
    • Popliteus
    • Flexor Digitorum Longus
    • Flexor Hallucis Longus
    • Tibialis Posterior
  • Lateral Compartment of the Leg
    • Fibularis Longus
    • Fibularis Brevis
  • Anterior Compartment of the Leg
    • Tibialis Anterior
    • Extensor Digitorum Longus
    • Extensor Hallucis Longus
    • Fibularis Tertius

9. Bones

  • Axial (midline)
    • Skull (midline)
    • Mandible (midline)
    • Manubrium (midline)
    • Xiphoid process (midline)
    • Vertebrae (midline)
      • Cervical vertebrae (midline)
        • C1 – C7 (midline)
      • Thoracic vertebrae (midline)
        • T1 – T12 (midline)
      • Lumbar vertebrae (midline)
        • L1 – L5 (midline)
      • Sacrum (midline)
        • S1 – S5 (midline)
      • Coccyx (midline)
  • Ribcage
    • Ribs
      • True ribs
        • R1 – R7
      • False ribs
        • R8 – R10
      • Floating ribs
        • R11 – R12
    • Sternum (midline)
    • Costal cartilage
  • Upper limb
    • Scapula
    • Clavicle
    • Humerus
    • Ulna
    • Radius
    • Bones hand (not yet expanded)
  • Lower limb
    • Coxal bone
      • Pubis
      • Ilium
      • Ischium
    • Femur
    • Patella
    • Tibia
    • Fibula
    • Bones foot (not yet expanded)