In this page you will find a set of brain templates constructed using fluid-attenuated inverse recovery (FLAIR) images, which can be used, for instance, to help to automatically identify white matter hyperintensities (WMH; e.g. leukoaraiosis, multiple sclerosis) from magnetic resonance images (MRI), or as target for registration of other individual FLAIR images without the need of a matching T1-weighted image, using software such as FSL and SPM.
Two versions are available, based on the full or on a restricted sample, each of these in three different resolutions (0.7 mm, 1.0 mm and 2.0 mm). The difference between the full sample and the restricted sample is that in the full sample, all subjects available at the time of the construction of the templates were used (N=853), whereas the restricted sample only subjects that presented none or the least volumes of white matter hyperintensities were used (see more details below). In addition to FLAIR, templates for gray matter (GM), white matter (WM), cerebrospinal fluid (CSF) and T1-weighted (T1) are also provided for both samples.
All templates can be downloaded in just one file, here: GG-all.tar (447 MB).
Information about the sample
Subjects are participants of the Genetics of Brain Structure and Function Study (GOBS), a collaborative effort involving the Texas Biomedical Research Institute, the Yale University School of Medicine and the University of Texas Health Science Center at San Antonio. The participants are of Mexican–American ascent, and members of extended families (pedigrees). For the full sample (N=853), the mean age was 43.85 years (std. dev.: 14.81, min.: 18, max.: 85), with 515 females. For the restricted sample (N=366), the mean age was 35.44 years (std. dev.: 11.11, min.: 18, max.: 69), with 205 females.
Information about the MRI acquisition protocol
The images were acquired in either of two Siemens magnetom Trio 3 T scanners, one of these being a also Tim system. The aquisition sequences were:
- The FLAIR (Fluid-Attenuated Inverse Recovery, T2-weighted) sequence used echo time (TE): 363 ms, inversion time (TI): 1800 ms, repetition time (TR): 5000 ms, flip angle 180°, echo train length: 221, voxel size: 0.5 x 0.5 x 1.0 mm.
- The MPRAGE (Magnetisation Prepared Rapid Gradient Echo, T1-weighted) sequence used TE: 3.04 ms, TI: 785 ms, TR: 2100 ms, flip angle 13°, voxel size: 0.8 x 0.8 x 0.8 mm. A total of 7 acquisitions were performed and averaged to improve the signal-to-noise ratio (SNR; details in Kochunov et al., 2006, and here).
Overview of the image processing
The templates were constructed as part of the pipeline described in Winkler et al. (2009) for segmentation of white matter hyperintensities. In short, the FLAIR and the T1-weighted images for each subject were coregistered to each other, corrected for magnetic field inhomogeneities, and normalised to the MNI template (from the Montreal Neurological Institute).
After normalisation, voxels belonging to the white matter were selected and used as reference for a global intensity normalisation, to ensure that all subjects would have similarly ranged intensities. The normalisation used only the central region of the image histogram, such that the effect of eventual lesions would have minimal or no impact on this step. The full sample template (N=853 subjects) was produced by averaging all the images, whereas the template with a restricted sample (N=366 subjects) used only those that contained few or no white matter hyperintensities.
All the image processing steps used the FLAIR Segmentation Toolbox described in Winkler et al. (2009), which runs on SPM5 software. The normalisation uses the Unified Segmentation Algorithm (Ashburner et al., 2005).
Projects using these templates
- FLAIR Segmentation Toolbox, by Anderson Winkler and colleagues, described here (no longer maintained).
- Clinical Toolbox for SPM, by Chris Rorden and colleagues, available here.
How to cite
If you use these templates in your research, please cite it as:
- Winkler AM, Kochunov P, Glahn DC. FLAIR Templates. Available at http://brainder.org.
- Ashburner J, Friston KJ. Unified segmentation. Neuroimage. 2005;26(3):839-51.
- Kochunov P, Lancaster JL, Glahn DC, Purdy D, Laird AR, Gao F, Fox P. Retrospective motion correction protocol for high-resolution anatomical MRI. Hum Brain Mapp. 2006 Dec;27(12):957-62.
- Winkler AM, Kochunov P, Dierschke NA, Lancaster JL, Fox PT, Glahn DC. An automatic segmentation tool for white matter hyperintensities using FLAIR and T1-weighted images. 15th Annual Meeting of the Organization for Human Brain Mapping, 18-23 June 2009, San Francisco, CA, USA.
These FLAIR templates are licensed under the MIT License, the full text of which is below:
Copyright (c) 2012 Anderson M. Winkler, Peter Kochunov, David C. Glahn.
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- 18.Apr.2019: Fixed the TE and TI in the description above for FLAIR (the values were reversed, and further, where it should have been 1.8 s, it was 1.8 ms). Thanks to the anonymous reviewer of a 3rd party paper who noticed the error.
- 27.Nov.2012: Updated the center of the coordinate system to match the anterior commissure (AC), making registration easier in certain applications. Thanks to Torben E. Lund (Aarhus University, Denmark) for pointing out.
- 25.Aug.2012: Templates updated to larger samples (N=853 and N=366), in three different resolutions (0.7, 1.0 and 2.0 mm), and available for FLAIR and T1-weighted modalities, as well as GM, WM and CSF partitions.
- 09.May.2011: First public release of the FLAIR templates, using two samples sizes (N=462 and N=181), with resolution of 1 mm.