The Skull (kapāla)
Towards the centre of the head-dress is found the kapāla ("skull"). Normally, the skull (or for that matter even just bone or hair) is considered inauspicious in Hindu tradition. Says Gautama
Cf. Gautama-dharmasūtra 9.16: na bhasma-keśa-tuṣa-kapālāmedhyāny adhitiṣṭhet
न भस्म-केश-तुष-कपालामेध्यान्यधितिष्ठेत्
Gautama even goes to the extent of saying that one should not even utter the ghastly/inauspicious name kapāla, but should rather circumvent its use by a surrogate word such as bhagāla (same word, but a little deformed). Gautama-dharmasūtra 9.22: kapālaṁ bhagālam iti [brūyāt]!
While what Gautama says is fine for general contexts, in our situation here, the context is totally different. Kapāla actually signifies the [Masculine] Principle Immaculate (Puruṣa). As we understand from Āyurveda: 'hard items like bones come to the child from the father, and soft items like skin, from the mother.' Says Suśruta:
Suśruta-saṁhitā 3.3.43:
garbhasya keśa-śmaśru-lomāsthi-nakha-danta-sirā-snāyu-dhamanī-retaḥ-prabhṛtīni sthirāṇi pitṛjāni.
गर्भस्य केश-श्मश्रु-लोमाऽस्थि-नख-दन्त-सिरा-स्नायु-धमनी-रेतः-प्रभृतीनि स्थिराणि पितृजानि
The kapāla, being a bone-like structure, is thus masculine. When a person dies, the flesh dissipates fast while the bones and the bony kapāla last. It is for this reason that the long lasting skull - a physical token of the Ever-Abiding Metaphysical Puruṣa Principle - is placed on the head by Naṭarāja.
The Brain and the Turīya
The presence of all these on the head of Naṭarāja is itself significant. As stated in Nārada-parivrājakopaniṣad, the head is the place of Turīya, "the Fourth [State]" (the other three being - the Wakeful, the Dream, and the Deep Sleep States). Nārada-parivrājakopaniṣad 25: turīyaṁ mūrdhni saṁsthitam. The head is accorded the supreme place (hence styled uttamānga- "the Best Limb") in Āyurveda also, as 'the very abode of all the vital airs.'
Caraka-saṁhitā 1.17.12:
prāṇāḥ prāṇabhṛtāṁ yatra śritās sarvendriyāṇi ca |
yad uttamāṅgam aṅgānāṁ śiras tad abhidhīyate ||
प्राणाः प्राणभृतां यत्र श्रितास् सर्वेन्द्रियाणि च ।
यद् उत्तमाङ्गम् अङ्गानां शिरस् तद् अभिधीयते ॥
The importance attached to the brain goes even farther, back into the age of the Vedic literature. Aitareya Āraṇyaka attaches supreme importance to the brain, as the source of all activity in fine. (Aitareya Āraṇyaka 2.1.4:
yac chiro'śrayat tac chiro'bhavat | tac chirasas śirastvaṁ | tā etāḥ śīrṣañc chriyaḥ śritās cakṣuḥ śrotraṁ mano vāk prāṇaḥ | śrayante'smiñc chriyo ya evam etac chirasaḥ śirastvaṁ veda
यच् छिरोऽश्रयत् तच् छिरोऽभवत् । तच् छिरसस् शिरस्त्वं । ता एताः शीर्षञ्च्छ्रियः श्रितास् चक्षुः श्रोत्रं मनो वाक् प्राणः । श्रयन्तेऽस्मिञ्च् छ्रियो य एवम् एतच् छिरसः शिरस्त्वं वेद).
The Gītā also refers to yogic practices wherein one "deposits" one's prāṇa in the crown. Bhagavad-gītā 8.12: mūrdhny ādhāyā''tmanaḥ prāṇam.