LONI: Laboratory of Neuro Imaging

ICBM Single Subject MRI Anatomical Template

  • About the Template
  • Overview
  • About the Minc Files

About the Template

The high definition structural brain template is the average of 27 T1 weighted MRI acquisitions from a single subject (from Montreal Neurological Institute database). The template is aligned within the stereotaxic space of the ICBM average template derived from that of Talairach and Tournoux (1988).

Cortical gyri, subcortical structures and the cerebellum have been delineated from the structural brain template and assigned a unique label.

The 3-D set of labels can be imported and registered onto the structural MRI of any individual subject through a fully automatic implementation of diverse software assembled in the specific module of the pipeline.


The ICBM (International Consortium for Brain Mapping) high-resolution single subject template is aligned with the individual subject T1 whole brain MRI provided.

An AIR (see the AIR software page for more information on AIR) nonlinear warp, a 5th order polynomial, is used for this fit. The demarcated labels on the template are then resampled through the warp transform to the subject MRI. A nearest-neighbor resampling is used to ensure the labels stay as labels. The 0.125mm3 resolution of the template helps ensure that the proper label, at least according to the transform, is used in the resampling.

About the Minc Files

The volumes are in minc format and can presently be visualized using the program Display. The download file needs to be unzipped. You can do this by typing: unzip ICBM_0.5mm.mnc.zip. To view both the structural MRI and the labels launch the program typing: Display ICBM_template.mnc -label ICBM_labels.mnc. The opacity of the labels can be set in the Colour Coding menu. The number of each label appears at the bottom left of the orthogonal views window. This number corresponds to a unique structurelisted in labels_text.


Download the ICBM Single Subject Template Atlas

Figure 1 - lateral (A) and medial (B) view of cortical labels displayed on the surface reconstruction of the left hemisphere.
Figure 2 - 3D models of main thalamic subdivisions reconstructed from the label volume.