In vivo human MRI at 0.35 mm reveals up to 15 ms T2* changes within gray matter across depths at 7T

Poster No:


Submission Type:

Abstract Submission 


Omer Faruk Gulban1,2, Saskia Bollmann3, Renzo Huber1, Kendrick Kay4, Benedikt Poser1, Federico De Martino1, Rainer Goebel1,2, Dimo Ivanov1


1Maastricht University, Maastricht, Netherlands, 2Brain Innovation, Maastricht, Netherlands, 3Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, 4University of Minnesota, Minneapolis, MN

First Author:

Omer Faruk Gulban  
Maastricht University|Brain Innovation
Maastricht, Netherlands|Maastricht, Netherlands


Saskia Bollmann  
Centre for Advanced Imaging, The University of Queensland
Brisbane, QLD
Renzo Huber  
Maastricht University
Maastricht, Netherlands
Kendrick Kay  
University of Minnesota
Minneapolis, MN
Benedikt Poser  
Maastricht University
Maastricht, Netherlands
Federico De Martino  
Maastricht University
Maastricht, Netherlands
Rainer Goebel  
Maastricht University|Brain Innovation
Maastricht, Netherlands|Maastricht, Netherlands
Dimo Ivanov  
Maastricht University
Maastricht, Netherlands


Mesoscopic in vivo human MRI (≤ 0.5 mm) has been used to reveal intracortical details [1, 2, 3, 4]. However, the region of focus has long been the calcarine sulcus (hosting primary visual cortex). Here, we extend mesoscopic in-vivo MRI in three ways:
1. We perform simultaneous quantitative imaging of Heschl's gyrus (hosting primary auditory cortex) in addition to the calcarine sulcus.
2. We develop tools optimized for partial-coverage anatomical imaging.
3. We report T2* changes as a function of cortical depth & orientation of the local cortex relative to B0 [5].


We acquired data from 5 volunteers at 7T (Siemens) using a 32-channel coil (Nova) and 3D ME-GRE with bipolar readout (350 μm iso. res.; TR = 30 ms; TE1-6= [3.83, 8.20, 12.57, 16.94, 21.31, 25.68] ms; α = 11°; elliptic k-space; 14 min., FOV = 201.6 × 201.6 × 36.4 mm3). 4 ME-GRE images were acquired. We changed the phase-encoding direction by 90° (RL, AP, LR, PA) in each acquisition. The 90°-changes were used to control the flow artifacts directions [6]. In a separate session, we acquired MP2RAGE (0.35 mm iso.; TR/TE/TI1/TI2 = 5000/2.91/800/2700 ms; α1/α2=4°/5°; FOV=200×200×36 mm3, 10 min × 8) for segmentation. We used dielectric pads [8]. See Fig 1 for coverage.

The flow artifacts were mitigated by compositing images with 90° phase-encoding changes [9]. We averaged & registered ME-GRE & MP2RAGE images. The final T1-w images have good WM-GM contrast. T2* maps show high sensitivity to microarchitecture (Stria of Gennari) and vascular features such as the intracortical vessels (Fig 1).

We segmented 4 regions: Heschl's gyri and calcarine sulci in both hemispheres. LayNii [10] LN2_LAYERS program was used to compute equi-volume cortical depths together with local cortex orientations for each gray matter voxel (0.35 mm iso. res.). We used LN2_MULTILATERATE program to grow surface disks of equal sizes centered on the macroanatomical landmarks. B0 vectors are used to compute the angle between local cortex orientations relative to the B0 vector (Fig 2).
Supporting Image: abstract-2_figure-1.png
   ·Figure 1. ME-GRE & MP2RAGE coverages near Heschl's gyrus and calcarine sulcus. Zoomed images for Heschl's gyrus and calcarine sulcus showing MP2RAGE UNI contrasts T2* obtained from ME-GRE.


We plot 2D histograms of T2* values across cortical depths for our regions of interest (Fig 2). These show that the striae of Gennari are clearly visible as a dip around the middle cortical depth in the T2* measurements. However, we do not see a similar layer pattern at Heschl's Gyri in either hemisphere. This observation highlights that even if the stria of Gennari is clearly visible in the calcarine sulcus, one cannot expect to see layer patterns of equal magnitude around Heschl's gyrus. This would speak for the uniqueness of the calcarine sulcus layering compared to the rest of the cortex.

We also plot 2D histograms of T2* across local surface orientations relative to the B0 vector (Fig 2). Although the orientations are sampled non-uniformly across the visual and auditory regions, we do not observe T2* fluctuations across different orientations comparable to the degree of T2* fluctuations across depths. This observation highlights the local biological tissue compositions has a stronger effect on T2* compared to the signal fluctuations due to B0 alignment. Noted that there are only a few samples from the most extreme B0 alignment configurations where the largest differences could be expected.
Supporting Image: abstract-2_figure-2.png
   ·Figure 2. Processing steps for our regions of interest together with depth metrics and B0 alignment. 2D histograms show T2* values as a function of cortical depths and B0 alignment of local surfaces.


Our results showed that gray matter T2* varies up to 15 ms (whole range typically being in between 25 to 45 ms) from deep to superficial layers. Stria of Gennari shows up as a major reduction of T2* within calcarine sulcus. However, a similar layering is not visible within Heschl's gyrus. B0 alignment effects seem not to be as strong as the biological tissue composition effects that are observed across the visual & auditory regions. Establishing a baseline of in vivo human brain T2* values as a function of other variation sources is needed to understand the MRI signal to set more plausible expectations about the required resolution and signal amplitude assumptions of the future (e.g. functional imaging).

Modeling and Analysis Methods:

Methods Development 2

Neuroanatomy, Physiology, Metabolism and Neurotransmission:

Cortical Anatomy and Brain Mapping
Neuroanatomy Other

Novel Imaging Acquisition Methods:

Anatomical MRI 1


Cortical Columns
Cortical Layers
Data analysis
Other - 7T

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?


Which processing packages did you use for your study?

Other, Please list  -   LayNii

Provide references using author date format

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[2] Duyn, J. H., van Gelderen, P., Li, T.-Q., ... Fukunaga, M. (2007). High-field MRI of brain cortical substructure based on signal phase. Proceedings of the National Academy of Sciences, 104(28), 11796–11801.

[3] Budde, J., Shajan, G., Hoffmann, J., Uǧurbil, K., & Pohmann, R. (2011). Human imaging at 9.4 T using T2*-, phase-, and susceptibility-weighted contrast. Magnetic Resonance in Medicine, 65(2), 544–550.

[4] Kemper, V. G., De Martino, F., Emmerling, T. C., Yacoub, E., & Goebel, R. (2018). High resolution data analysis strategies for mesoscale human functional MRI at 7 and 9.4T. NeuroImage, 164, 48–58.

[5] Cohen-Adad, J., Polimeni, J. R., Helmer, K. G., Benner, T., McNab, J. A., Wald, L. L., Rosen, B. R., Mainero, C. (2012). T2* mapping and B0 orientation-dependence at 7T reveal cyto- and myeloarchitecture organization of the human cortex. NeuroImage, 60(2), 1006–1014.

[6] 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), 1117–1124.

[7] Cohen-Adad, J., Polimeni, J. R., Helmer, K. G., Benner, T., McNab, J. A., Wald, L. L., … Mainero, C. (2012). T 2* mapping and B 0 orientation-dependence at 7T reveal cyto- and myeloarchitecture organization of the human cortex. NeuroImage, 60(2), 1006–1014.

[8] Teeuwisse, W. M., Brink, W. M., & Webb, A. G. (2012). Quantitative assessment of the effects of high-permittivity pads in 7 Tesla MRI of the brain. Magnetic Resonance in Medicine, 67(5), 1285–1293.

[9] Gulban, O. F. (2020). Chapter 6: In vivo T2* imaging of human auditory cortex at 350 μm isotropic resolution. Imaging the human auditory system at ultrahigh magnetic fields. ProefschriftMaken.

[10] Huber, L., ... Gulban, O. F. (2020). LayNii: A software suite for layer-fMRI. BioRxiv.