Its similar to the binding ritual performed by ritualists on spirits. In this process a part of soul and spirit energy of a person is separated and is binded into a body part. The part will get transmuted become a white stone called scrims.
In most cases the bones that have no particular function to body are used. Bones being denser can store more energy. But ones the transmutation happens that part of the body become useless. As a result Vestigial organs were the main organs that were usually transmuted.
Also in some cases blood is sometimes used to make scrims, A person is bled and a blood manipulator is bought in to condense it so as to help it transmute into scrims. As time passed scrim was solely made by blood except.
Scrims are gems formed as a result of transmutation process with the help of runes. The gem so formed can be used to activate a particular wave to which it is connected.