Cerebellar surface mapping using T1 and T2* relaxometry at ultrahigh-field MRI: from  macroscale to microscale?
Yohan Boillat1, Pierre-Louis Bazin2, Kieran O'Brien3,4, Mário João Fartaria de Oliveira5,6, Guillaume Bonnier1,6,7, Gunnar Krueger6,8, Wietske van der Zwaag1,9, and Cristina Granziera1,6,7,10

1Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland, 2Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, 3Siemens Healthcare Pty Ltd., Brisbane, Australia, 4University of Queensland, St-Lucia, Australia, 5University of Lausanne, Lausanne, Switzerland, 6Advanced Clinical Imaging Technology Group, Siemens, Lausanne, Switzerland, 7Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland, 8Healthcare Sector IM&WS S, Siemens Schweiz AG, Lausanne, Switzerland, 9Spinoza Centre for Neuroimaging, Amsterdam, Switzerland, 10Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States


The quantitative properties of the cerebellum were assessed by acquiring T1 and T2*contrasts at 7T and mapping these onto the cerebellar cortex. T1 maps showed medial-lateral alternating stripes of different intensities while T2* values were homogeneously distributed across the lobes. This study showed the heterogeneity of the cerebellar cortex in terms of tissue content, which in part parallels a well-established gene expression pattern.

Target audience

Neuroscientists and physicists interested in the cerebellum and its quantitative properties


The purpose of this study was to map T1 and T2*values on the cerebellar surface. The cerebellum is usually considered to have a relatively homogenous cortex in contrast to the cytoarchitectonic heterogeneity of the neocortex. Nevertheless, the cerebellar cortex is heterogeneous in terms of gene expression (e.g. zebrin II pattern), function and microcircuitry activity pattern1,2. The regional cortical properties of the cerebellum have been so far studied using microscale techniques such as electrophysiology and immunochemistry3,4. Whether microscale patterns can be seen at the submillimeter scale, as provided by ultra-high field MRI, is still unknown. Here, we performed surface analysis of the cerebellar cortex using quantitative T1 and T2*maps acquired at 7TMRI.


Nine healthy participants (2 females, age=31±7), took part in the study. Whole-brain T1 and T2*maps were acquired using the MP2RAGE5 (TR/TE/TI1/TI2 6000/2.84/750/2350ms, matrix:300x320x160, 0.75x0.75x0.9mm3) and 3D multi gradient echo (MGE; TR 45ms TE1/ΔTE/TE9 4.59/4.59/41.3ms, matrix:300x320x160, 0.75x0.75x0.9mm3) sequences at 7T (Siemens, Germany) using a 32 channel head coil (Nova USA). Three dielectric pads were placed around the upper neck to improve the inversion efficiency over the cerebellum and whole brain B1 homogeneity. A mono-exponential fit to the MGE data was used to obtain the T2*maps. T2*was registered to the MP2RAGE using Elastix6. A SA2RAGE B1 map7 was acquired (TR/TE 2400/0.72ms, matrix:116x128x64, 2.3x2.3x4mm, same transmit voltage as MP2RAGE) to correct the MP2RAGE for B1 homogeneity8. The corrected T1 map was used for all the following steps. The tools used for the image processing were part of the CBS tools9. Both T1 and T2*maps were brought into the MNI space. The T1 images were subsequently segmented using the multi-geometric deformable model segmentation algorithm9. The central cerebellar surface (middle gray matter layer) was extracted with an adaptation of the CRUISE algorithm10 which preserves the surface topology of the cerebellum. A diffeomorphic image registration algorithm11 was used to realign the T1 volumes to a high-resolution template from the CBS Tools. Transformation maps were obtained from the previous procedure and applied for the geometric averaging of the surfaces and the mapping of the T1 and T2*values.


The geometric average of the 9 cerebellar surfaces allows the labelling of the different cerebellar (Figure 1) because of the precise segmentation and surface alignment. In the average T1 cortical surface, T1 values were higher around the vermis as well as in the fissures, while the folia showed lower values (Figure 2). Most interestingly, the T1 values of the folia appeared to have a pattern of medial-lateral alternating stripes of higher and lower T1 values (Figure 2). More precisely, the most medial and most lateral part of the hemispheres had similar values and the T1 was lower in the longitudinal middle part of a single hemisphere. The T2*surface displayed different patterns (Figure 3). The superior lobe of the cerebellum had higher T2*values compared to the more inferior lobes. Whether there is a media-lateral alternating pattern for T2*values following the folia of the middle lobe in a medio-lateral fashion is more difficult to observe. However, an increase of T2*can be seen when moving from the posterior to the anterior side (Figure 3). Moreover, some dots representing high T2*values in the superior lobe seem to be vaguely aligned with the blue pattern in Figure 2.


While for most of the cerebellar cortical surface quantitative T1 and T2* could be obtained with high confidence, the very low T1 values in the most inferior area are likely due to loss of SNR and correspondingly poor T1 estimates. Similarly, reduced T2*values in the inferior lobules might indicate a non-perfect B0 shim. We identified two distinguishable patterns arising from the in vivo quantitative mapping. T1 maps showed longitudinal stripes while T2*values appeared to be more homogeneously distributed across the lobes. In both contrasts, there was an intensity difference between the folia and the fissures. The alternating longitudinal pattern was very similar to the well-known zebrin II (also called aldolase C) pattern in rodent cerebelli4. The latter has been shown to have tight relationship with incoming climbing fibers12. Although still hypothetical, the observed contrast could be linked to the amount of input myelinated axons as T1 contrast is known to be sensitive to myelination13.


This study showed for the first time in MRI various topographic changes in tissue properties in the cerebellum, using high-resolution quantitative acquisitions at 7T. A possible cause for sagittal T1 zones might be found in the presence of Zebrin regions, opening a window towards finer differentiation of cerebellar architecture in vivo.


No acknowledgement found.


1. Cerminara, N. L., Lang, E. J., Sillitoe, R. V. & Apps, R. Redefining the cerebellar cortex as an assembly of non-uniform Purkinje cell microcircuits. Nat. Rev. Neurosci. 16, 79–93 (2015).

2. Apps, R. & Hawkes, R. Cerebellar cortical organization: a one-map hypothesis. Nat. Rev. Neurosci. 10, 670–681 (2009).

3. Hawkes, R. Purkinje cell stripes and long-term depression at the parallel fiber-Purkinje cell synapse. Front. Syst. Neurosci. 8, 41 (2014).

4. Marzban, H. & Hawkes, R. On the architecture of the posterior zone of the cerebellum. Cerebellum 10, 422–434 (2011).

5. Marques, J. P. et al. MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. Neuroimage 49, 1271–81 (2010).

6. Klein, S., Staring, M., Murphy, K., Viergever, M. a. & Pluim, J. elastix: A Toolbox for Intensity-Based Medical Image Registration. IEEE Trans. Med. Imaging 29, 196–205 (2010).

7. Eggenschwiler, F., Kober, T., Magill, A. W., Gruetter, R. & Marques, J. P. SA2RAGE: a new sequence for fast B1+ -mapping. Magn. Reson. Med. 67, 1609–19 (2012).

8. Marques, J. P. & Gruetter, R. New developments and applications of the MP2RAGE sequence--focusing the contrast and high spatial resolution R1 mapping. PLoS One 8, e69294 (2013).

9. Bazin, P. L. et al. A computational framework for ultra-high resolution cortical segmentation at 7 Tesla. Neuroimage 93, 201–209 (2013).

10. Han, X. et al. CRUISE: Cortical reconstruction using implicit surface evolution. Neuroimage 23, 997–1012 (2004).

11. Avants, B. B., Epstein, C. L., Grossman, M. & Gee, J. C. Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain. Med. Image Anal. 12, 26–41 (2008).

12. Fujita, H. & Sugihara, I. Branching patterns of olivocerebellar axons in relation to the compartmental organization of the cerebellum. Front. Neural Circuits 7, 1–9 (2013).

13. Lutti, A., Dick, F., Sereno, M. I. & Weiskopf, N. Using high-resolution quantitative mapping of R1 as an index of cortical myelination. Neuroimage 93, 176–188 (2014).


Figure 1 Average of the individual surfaces mapped with a lobule atlas. a) Posterior view of the cerebellum. b) Lateral view of the cerebellum.

Figure 2 Average of the individual surfaces mapped with the averaged T1 values. a) Posterior view of the cerebellum. b) Lateral view of the cerebellum. c) Superior view of the cerebellum.

Figure 3 Average of the individual surfaces mapped with the averaged T2 * values. a) Posterior view of the cerebellum. b) Lateral view of the cerebellum. c) Superior view of the cerebellum.

Proc. Intl. Soc. Mag. Reson. Med. 24 (2016)