MRI Brain Template

Contacts
Pierre Jannin Pierre.Jannin@irisa.fr
Florent Lalys Florent.Lalys@irisa.fr

Here you can download the images files of the MRI T1 template, T2 Template and T1/T2 mixed template which are made freely available to our community. The resulting T1 volume was computed from 15 acquisitions of the same subject. The resulting T2 from 7 acquisitions.

These templates were created in order to improve visualization of spatially complex deep brain structures such as basal ganglia. They can used as a reference for neuroimage processing methods.

The strategy used for building the templates is described in (Lalys F, Haegelen C, Ferre JC, El-Ganaoui O, Jannin P.; Construction and assessment of a 3-T MRI brain template.; Neuroimage; August 2009). All native images were first denoised with the Non-Local Means algorithm (Coupé et al., /IEEE trans on Medical Imaging, 2008), then a step of inhomogeneity correction was applied (Mangin, IEEE press, 2000). All T1 and T2 volumes were registered to a reference image (randomly chosen among the native images) and averaged with the kappa-sigma clipping method (kappa=1.8). For the construction of the T1-T2 mixed template, a Region of Interest including basal ganglia was kept from the T2, then intensity inversed, and finally merged with the remaining T1 average volume.
Additional data based on these templates will be soon available: all original DICOM images, segmented structures, ...

Here is the table of the whole available data :

Templates	Nifti format	GIS format	Analyze format	Informations
T1 Template at native resolution	Nifti	GIS	Analyze	Infos : dimensions are 512 x 512 x 182
T1 Template at high resolution	Nifti	GIS	Analyze	Infos : dimensions are 1024 x 1024 x 364
T2 Template at native resolution	Nifti	GIS	Analyze	Infos : dimensions are 512 x 512 x 182
T2 Template at high resolution	Nifti	GIS	Analyze	Infos : dimensions are 1024 x 1024 x 364
T1/T2 mixed template at native resolution	Nifti	GIS	Analyze	Infos : dimensions are 512 x 512 x 182
T1/T2 mixed template at high resolution	Nifti	GIS	Analyze	Infos : dimensions are 1024 x 1024 x 364

If you use these templates, please cite : Lalys F, Haegelen C, Ferre JC, El-Ganaoui O, Jannin P.; Construction and assessment of a 3-T MRI brain template.; Neuroimage; August 2009.

MRI Template - T1 + T2

Contacts
Pierre Jannin Pierre.Jannin@irisa.fr
Florent Lalys Florent.Lalys@irisa.fr
Alexandre Abadie (Administrator) Alexandre.Abadie@irisa.fr