Shortly

It seems French simply uses "calibrage", without anymore specification.

If you want to be more precise, you may say you calibrated the machine by using fiducial markers : "Le calibrage se fait en utilisant des marqueurs."

Your other proposals

About "calibration fiducial"

Forget it. "Fiducial" does not seem to exist in French (according to the Wiktionnaire).

As for "calibration", I'd personnally go for "calibrage" or "étalonnage".

"Étalonnage" seems great because it refers to an "étalon", a reference, which the fiducial markers are. But this is still the uneducated guess.

About "conventionnel"

You are correct again: this seems ill-adapted to this context and may lead to misundestandingsmisunderstandings, "conventionnel" being heard as "conventional" or "standard".

Search/thought process

Fiducial markers

I looked for a translation of "fiducial marker" and found "marqueur de calibrage". Here is a definition that seems to match your own:

Plus spécifiquement, un marqueur de calibrage est un objet radio-opaque ayant un diamètre approximatif de 25 mm. Il s’agit généralement d’une boule de métal installée au bout d’une tige flexible. La tige permet de positionner l’objet dans le plan anatomique recherché.

From the marker to the calibration

On the same page, the calibration process is quickly spoken of (emphasis is mine):

Un marqueur de calibrage est parfois appelé un marqueur mise à l’échelle. Pour plus d’informations au sujet du calibrage (ou de la mise à l’échelle)

_{Disclaimer: I am not a physicist. Someone may know better than me.}