The study of disorders of consciousness (DoC) is very complex because patients suffer from a wide variety of lesions, affected brain mechanisms, different severity of symptoms, and are unable to communicate. Combining neuroimaging data and mathematical modeling can help us quantify and better describe some of these alterations. The goal of this study is to provide a new analysis and modeling pipeline for fMRI data leading to new diagnosis and prognosis biomarkers at the individual patient level. To do so, we project patients' fMRI data into a low-dimension latent-space. We define the latent space's dimension as the smallest dimension able to maintain the complexity, non-linearities, and information carried by the data, according to different criteria that we detail in the first part. This dimensionality reduction procedure then allows us to build biologically inspired latent whole-brain models that can be calibrated at the single-patient level. In particular, we propose a new model inspired by the regulation of neuronal activity by astrocytes in the brain. This modeling procedure leads to two types of model-based biomarkers (MBBs) that provide novel insight at different levels: (1) the connectivity matrices bring us information about the severity of the patient's diagnosis, and, (2) the local node parameters correlate to the patient's etiology, age and prognosis. Altogether, this study offers a new data processing framework for resting-state fMRI which provides crucial information regarding DoC patients diagnosis and prognosis. Finally, this analysis pipeline could be applied to other neurological conditions.