Some of the processes offered by BrainVISA automatically generate transformation files and apply different coordinate systems to objects, the Talairach-MNI template-SPM or the Talairach-AC/PC-Anatomist referentials for instance. This files are automatically loaded by BrainVISA when Anatomist is called. Then, BrainVISA scans transformation files linked to every object it loads in Anatomist (0 or severals files can be found). Only one transformation file is loaded according to a priority if there are several ones:
Talairach-MNI template-SPM: the file corresponding to this transformation is RawT1-<subject>_<acquisition>_TO_Talairach-MNI.trm. It is computed for example when you use a normalization instead of manually selected AC/PC coordinates in the Morphlogist pipeline.
Talairach-AC/PC-Anatomist: the transformation file linked to this referential is RawT1-<subject>_<acquisition>_TO_Talairach-ACPC.trm. When you use T1 MRI -> Morphologist pipeline, this file is implicitly generated. The Prepare Subject process is always run before the anatomical pipeline, to make sure that the axial, coronal and sagittal orientations and the radiological convention of the T1 volume are correct. This process allows you to place several points (AC, PC and IP), so that you know exactly where you are in the volume. This file contains the data required to switch from the referential system of the image to a Talairach system (in this case, based on the AC and PC points defined in the Prepare Subject process).
Globally Registred SPAM Referential: this referential is related to the automatic identification of the cortical sulci using the SPAM method.
Other referential: If there is a unique path to another referential, the corresponding transformation is loaded. It could be a transformation between two modalities for the same subject for example.
Object Referential : if no transformation file is linked to the loaded object, no information will be given to Anatomist and this object will be in its own coordinate system.