9.4T MRI reveals mesoscopic cortical gray matter vasculature in vivo

Poster No:


Submission Type:

Abstract Submission 


Omer Faruk Gulban1, Valentin Kemper1, Dimo Ivanov1, Benedikt Poser1, Federico De Martino1


1Maastricht University, Maastricht, Netherlands



Ultra high field (UHF,>7T) magnetic resonance imaging (MRI) provides an exciting venue to push the boundaries of in-vivo anatomical human brain imaging. There have been a few recent promising demonstrations to acquire mesoscopic (<500μm) resolution in-vivo anatomical images at UHF [Lusebrink2017,Mattern2018]. Here we use a 9.4T MRI scanner using parallel radio frequency transmission (pTX) technology with a custom built coil to acquire multi-echo gradient echo (ME-GRE) anatomical images of the superior temporal cortex of a living human brain at 350μm isotropic resolution. Our motivation is to expand in-vivo human imaging territory towards what is possible to do with ex-vivo methods.


A volunteer (39, male) was scanned in 2 sessions at 9.4T MRI scanner (Siemens) at Maastricht University. ME-GRE images at 350μm iso. resolution (TR=30ms, TE=[4.7,8.7,12.8,16.8,20.8,24.8]ms, 458x294x96, 14min dur.) were acquired using a custom coil with 8Tx/24Rx (LifeServices, Inc, MN), in-house implementation [Tse2016] of 3-spoke slab-selective pTX excitation [Setsompop2008]. In total, 8 successful ME-GRE images were acquired.

Magnitude images from both sessions were processed by initially aligning them using ITK-SNAP interactive registration, followed by mask-based automatic registration for fine alignment. The fine alignment mask was drawn on both hemispheres as a large sphere centered at the lateral part of the sup. temp. cortex but not including skull tissue. Voxels that are not present within the field of view in both sessions were masked out. A strong multi-image bias field correction was applied (inspired by [Petro2014], generalized to n-dimensions to account for >3 echos). This step was followed by percentile-based dynamic range clipping to equalize intensities across sessions. All images were averaged across sessions and echos to create a single image. The mean image was segmented manually to create a cerebrum mask around the maximally visible portions of the brain (sup. temp. cortex around Heschl's Gyrus). This cerebrum mask was used to create an outer gray matter surface. In addition, we segmented the macroscopic arteries from the image at TE=4.7ms, and reconstructed arterial surfaces. Both of these surfaces can be seen in Fig.2A. To visualize penetrating gray matter mesoscopic vessels, we generated another surface by moving each vertex of the outer gray matter surface along their normals toward white matter by 500μm. This surface was used to sample image within gray matter intensities (Fig.2B).
Supporting Image: figure_1.png
   ·Figure 1. Coronal view of dynamic range normalized sum of all echos. The yellow marks indicate a few penetrating gray matter vessels.


Our images show exquisite detail around superior temporal cortex (Fig.1). Many penetrating gray matter vessels are visible to the naked eye and vanish at white matter boundary. In addition to vascular structures, lamination patterns within gray matter are also visible, albeit less clear in comparison. When observed in relation to the macroscopic arteries the spatial misregistration of vascular MR signal due to flow [Larson1990] becomes apparent (Fig.2A). The bright signal originating from within the artery shifts towards its flow direction vector component along the phase encoding direction and leaves behind no signal (see dark shades). The within gray matter surface sampling (Fig.2B) shows the penetrating gray matter vessels as dark spots. Penetrating vessels (~350μm diameter) appear somewhat regularly spaced with some variation in density when looked from medial to lateral axis.
Supporting Image: figure_2.png
   ·Figure 2. Gray matter surface intensities visualized in 3D bird’s eye view together with macroscopic arteries (A). Within gray matter intensities present penetrating vessels in 3D (B).


We show that imaging mesoscopic vasculature within cortical gray matter is within reach of in-vivo UHF MRI. Ability to do so in individual brains has potentially important implications for hemodynamic modelling [Uludag2018] and signal interpretation in layer fMRI [Ahveninen2016,Kay2018,Moerel2017]. Another potential area of inquiry is the relation between penetrating vessel lengths and cortical thickness. These vessel lengths might be useful in brain regions where it is hard to see the white-gray matter boundary such as the motor cortex or primary visual/auditory cortex.

Imaging Methods:

Anatomical MRI 1

Modeling and Analysis Methods:

Other Methods


Neuroanatomy Other 2


Other - vasculature

1|2Indicates the priority used for review

My abstract is being submitted as a Software Demonstration.


Please indicate below if your study was a "resting state" or "task-activation” study.


Healthy subjects only or patients (note that patient studies may also involve healthy subjects):

Healthy subjects

Was any human subjects research approved by the relevant Institutional Review Board or ethics panel? NOTE: Any human subjects studies without IRB approval will be automatically rejected.


Was any animal research approved by the relevant IACUC or other animal research panel? NOTE: Any animal studies without IACUC approval will be automatically rejected.

Not applicable

Please indicate which methods were used in your research:

Structural MRI

For human MRI, what field strength scanner do you use?

If Other, please list  -   9.4T

Which processing packages did you use for your study?

Brain Voyager

Provide references using author date format

Ahveninen, J., Chang, W. T., Huang, S., Keil, B., Kopco, N., Rossi, S., … Polimeni, J. R. (2016). Intracortical depth analyses of frequency-sensitive regions of human auditory cortex using 7T fMRI. NeuroImage, 143, 116–127.

Kay, K., Jamison, K., Vizioli, L., Zhang, R., Margalit, E., & Ugurbil, K. (2018). A critical assessment of data quality and venous effects in ultra-high-resolution fMRI. BioRxiv.

Larson, T. C., Kelly, W. M., Ehman, R. L., & Wehrli, F. W. (1990). Spatial misregistration of vascular flow during MR imaging of the CNS: cause and clinical significance. AJR. American Journal of Roentgenology, 155(5), 1117–24.

Lüsebrink, F., Sciarra, A., Mattern, H., Yakupov, R., & Speck, O. (2017). T1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm. Scientific data, 4, 170032.

Mattern, H., Sciarra, A., Lüsebrink, F., Acosta‐Cabronero, J., & Speck, O. (2018). Prospective motion correction improves high‐resolution quantitative susceptibility mapping at 7T. Magnetic resonance in medicine.

Moerel, M., De Martino, F., Kemper, V. G., Schmitter, S., Vu, A. T., Uğurbil, K., … Yacoub, E. (2018). Sensitivity and specificity considerations for fMRI encoding, decoding, and mapping of auditory cortex at ultra-high field. NeuroImage, 164(March 2017), 18–31.

Petro, A. B., Sbert, C., & Morel, J. (2014). Multiscale Retinex. Image Processing On Line, 4, 71–88. http://doi.org/10.5201/ipol.2014.107

Setsompop, K., Alagappan, V., Gagoski, B., Witzel, T., Polimeni, J., Potthast, A., … Adalsteinsson, E. (2008). Slice-selective RF pulses for in vivo B1+ inhomogeneity mitigation at 7 Tesla using parallel RF excitation with a 16-element coil. Magnetic Resonance in Medicine, 60(6), 1422–1432.

Tse, D. H. Y., Wiggins, C. J., Ivanov, D., Brenner, D., Hoffmann, J., Mirkes, C., … Poser, B. A. (2016). Volumetric imaging with homogenised excitation and static field at 9.4 T. Magnetic Resonance Materials in Physics, Biology and Medicine, 29(3), 333–345.

Uludag, K., & Blinder, P. (2018). Linking brain vascular physiology to hemodynamic response in ultra-high field MRI. NeuroImage, 168(December 2016), 279–295.