Some of the processes offered by BrainVISA automatically generate transformation files and apply different coordinate systems to objects, the spm_template referential or the Talairach referential 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:
spm_template referential (1st): the file corresponding to this transformation is either anat_subject_sn3d_TO_spm_template.trm for SPM99 or anat_subject_sn_TO_spm_template.trm for SPM2. This file is obtained by converters -> automatic -> SPM sn3d to AIMS transformation converter process (conversion of a normalization file (*sn3d.mat or *_sn.mat) generated by the SPM program into a .trm file that can be read by Anatomist and BrainVISA). This process is usable only if you have Matlab software installed and if BrainVISA is correctly setup to use it. This means the displayed coordinate system is the "normalized SPM".
Talairach referential (2nd) : the transformation file linked to this referential is subject_TO_Talairach.trm. When you use anatomy -> T1 Pipeline 2004 -> pipeline -> Ana Do A Lot of Things from T1 MRI process, this file is implicitly generated. The Prepare Subject process is always run before the anatomical pipeline process, 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. When the anatomical pipeline process is run, a transformation file (subject_TO_Talairach.trm) is created. 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).
Object Referential (3rd) : 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.
NOTE 1: Therefore, there are three possible situations, which will be handled in the following order of priority (if the file exists, the data are loaded): data contained in anat_subject_sn*_TO_spm_template.trm, otherwise data contained in subject_TO_Talairach.trm, otherwise no transformation (the object will be in its own referential system).
NOTE 2: The spm_template referential has a higher priority, i.e. if BrainVISA has to load an object A with the Talairach system and an object B with the spm_template referential, it will also load a Talairach_TO_spm_template transformation file to make sure that all the objects are contained in the spm_template referential.