SS-SI VASO pitfalls in visual cortex

Activation maps for BOLD and VASO. At about 0.8 mm resolution, one starts to see that VASO is less sensitive to large draining veins.

With respect to high-resolution VASO application, visual cortex is very unique. Because of its high demand, the most important pitfalls of SS-SI VASO in visual cortex are discussed below.

Anatomical challenges

Visual cortex is one of the thinnest cortical areas there are. Its about 1.8-2 mm thick and it is highly convoluted. Hence it is not straight forward to separate superficial and deeper layers.

In monkey V1, I successively increase the resolution further and further and only at about 0.5 mm voxels, I started to see the deeper layer IV. for comparison, in M1, layers can be visually separated at about 0.8 mm resolutions and higher.

Monkey V1. BOLD and CBV results. Even at 0.5 mm, a clear peak in the middle layer is not visible.

The higher spatial specificity of VASO compared to BOLD start of become visible at about 0.8-0.9mm resolutions.

Because V1 is so heavily convoluted, isotropic voxels must be used.

Physiological challenges

The visual cortex has the longest arterial arrival times compared to any other cortical area. Hence the inflow-effects (see also section of inflow effects here) are relatively easy to avoid.

However, we still saw some occurrences of inflow effects. Since inflowing blood magnetization is in equilibrium, the contaminated voxels are very bright. In my personal experience this could happen when participants have an unfortunate head position. It helps when they have their chin on their chest.

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These inflow effects of large arterial vessels are usually not very challenging in fMRI. 1.) They can be easily identifies and removed. 2.) These voxels are refilled with fresh blood with activation and rest conditions. So, they do not contaminate the functional contrast.

To be on the save side, I would advise a inversion-pulse phase skip of 30% and a inversion pulse amplitude above 90% (if SAR allows).

Readout challenges




Analysis challenges

Motion correction

Good protocols

We had good experiences with the following two protocols:

  • tilted axial, phase encoding direction A>>P, 0.8×0.8×1 mm resolution, PF 6/8, with 8 iterations POCS, 22 slices, TE 24ms, TR = 2296, strong fat sat, phase skip 30, FLASH GRAPPA 3 in plane.
  • tilted axial, phase encoding direction A>>P, 0.8×0.8×0.8 mm resolution, PF 6/8 with 8 iteration POCS, 22 slices, TE 24ms, TR = 2535, strong fat sat, phase skip 30, FLASH GRAPPA 3 x 2, with CAIPI 1/2.

A complete list with all used parameters is given here:

Availability of the sequence.

For high-resolution applications, I would highly recommend to use the VASO preparation in combination with a 3D-EPI readout. This sequence is largely implemented from Ben Poser and the binaries can be shared with everyone via C2P. The sequence is developed for VB17. If you are interested in the binaries, contact me via are in the process fighting for a VE11 version too. If you want to include your name on our petition, please let me know.

Gentle reminder

The CNR of VASO it 50%-60% of that of BOLD.


I thank Eli Merriam, Zvi Roth and Yuhui Chai for the pleasure of working with them on VASO in V1.