Standardized in QMRITools
Muscle segmentation naming
All muscles and bones that are segmented with QMRITools have a standardized name and number. The labels are stored as ITK-SNAP label description files in the folder NeuralNetworks of the toolbox (GitHub), and are used for manual segmentation, training of the networks and the output of SegmentData. The same names and numbers are used in the Muscle-BIDS pipeline.
Label files
| file | content | labels |
|---|---|---|
S1_Muscles_body_side | full body muscles and bones, left and right separate. This is the default output of SegmentData. | 261 |
S2_Muscles_leg_side | lower leg, upper leg and hip muscles, bones and fat, left and right separate | 105 |
S3_Muscles_shoulder_side | shoulder muscles and bones, left and right separate | 41 |
S4_Muscles_arm_upper_side | upper arm muscles and bones, left and right separate | 11 |
T1_Muscles_body | full body muscles and bones without left and right | 137 |
T2_Muscles_leg | lower extremity muscles and bones without left and right | |
N1 to N7 | label sets used for training the networks per region |
Numbering of the full body labels (S1)
In the full body label set every label has a three digit number region * 100 + index, where the region is the first digit and the index runs through the muscles of that region. Left and right muscles are consecutive, where odd numbers are left and even numbers are right. For example, 521 is the left vastus intermedius, and 522 the right vastus intermedius. Midline structures such as the bones in region 9 have a single number. The first digit is the body region:
| region | body part | examples |
|---|---|---|
| 1 | Head and neck | tongue, masseter, temporalis, scalenes, sternocleidomastoid |
| 2 | Shoulder | trapezius, deltoid, rotator cuff, pectoralis, serratus anterior |
| 3 | Back, thorax and abdomen | erector spinae, obliques, rectus abdominis, psoas major |
| 4 | Hip | gluteus maximus, medius and minimus, piriformis, levator ani |
| 5 | Upper leg | hamstrings, adductors, quadriceps, sartorius, gracilis |
| 6 | Lower leg | gastrocnemius, soleus, tibialis anterior, fibularis |
| 7 | Arm | biceps brachii, triceps brachii, forearm flexors and extensors |
| 8 | Bones, left and right | scapula, humerus, femur, tibia, fibula, ribs |
| 9 | Bones, midline | skull, mandible, sternum, vertebrae, sacrum |
The numbers in the other files (S2 to S4) are running numbers within that label file (for example 1 and 2 are the left and right lateral gastrocnemius in S2), so labels from different files should not be compared by number. The files with the suffix _side have the muscle name followed by Left or Right.
Use in QMRITools
The label files are used to translate between label numbers and names. By default the leg label file of the toolbox is used, and any ITK-SNAP label file can be given.
MuscleLabelToName[{1, 2, 3}]
MuscleNameToLabel[{"Soleus Left"}]
MuscleLabelToName[{501, 502}, labelFile]
Which output label set is used is selected with the what argument of SegmentData, see the segmentation page.