Documentation of Installing an IDEA VirtualBox for VE11 from OVA

This post documents the installation of an IDEA VE11 virtual box on a mac as done on May 14th 2018

Big thanks to Andy for figuring out how this works

Prerequisites

  • Here I start with a already built images of IDEA on windows vista and mars on Ubuntu. the images from FMRIF can be taken from erbium.nimh.nih.gov:/fmrif/projects/SiemensIdea/virtual_machines/OVF/): IDEA_ve11c-mars.ova and IDEA_ve11c+vd13d+vd13a.ova
  • Virtual box software can be downloaded here.

Continue reading “Documentation of Installing an IDEA VirtualBox for VE11 from OVA”

EPI phase correction algorithms

At high resolution EPI, the gradients are pushed to their limits and the ramp sampling ratio is particularly large. This means that the ghosting is increased and the Nyquist ghost correction is getting more important. In this post, I describe how to change the Nyquist ghost correction algorithm.

Phase_correction.gif
The high ramp sampling ratio in high-resolution EPI results in larger ghosts. Changing the correction algorithm from “normal” to “local” can help a lot.

Continue reading “EPI phase correction algorithms”

SS-SI VASO pitfalls in visual cortex

image125.gif
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.

Continue reading “SS-SI VASO pitfalls in visual cortex”

Partial-Fourier imaging at High Resolutions

This blog post discusses the resolution loss when applying partial-Fourier imaging in GE-EPI in the presence of strong T2*-decay.

I found that that when I was aiming for high-resolutions, it is beneficial to refrain from the application of partial Fourier (PF) imaging as much as possible. For the long readout durations at high-resolutions and the fast T2/T2*-decay at high field strengths results in even stronger blurring of partial-Fourier.

Continue reading “Partial-Fourier imaging at High Resolutions”

Finding ROI of the double layers in M1

In this post I want to describe the guidelines that helped me to find the right spot of primary motor cortex (M1) that has a double-layer pattern during a conventional finger tapping task.

The motor cortex is an excellent model system to debug-layer fMRI methodology for multiple reasons:

  1. It has a consistent folding pattern across people.
  2. Its folding pattern is convoluted across one axis only. Hence, it is possible to use thicker slices with higher in-plane resolution.
  3. With 4mm, its is the thickest part of the cortex compared to all other areas. Hence, layer analysis can be done even with 1.2 mm voxels.
  4. It has an expected double layer structure, with two separate peaks. The separability of the peaks can be used as a measure of functional specificity.
  5. It is very close to the RF-receive coils and has high tSNR.
  6. It is easy to shim.

One tricky part, however, is to find the right location of the double layer feature.

Continue reading “Finding ROI of the double layers in M1”

Gradient Temperature

tSNR changes across time

I got interested in gradient temperature because of the weird effect that tSNR seemed to increase over time.

Upon posing this effect on Twitter, PracitalfMRI and Ben Poser suggested that it might be due to gradient temperature. So I learned how to track it with as described below.

Continue reading “Gradient Temperature”

GRAPPA kernel size

Almost every modern fMRI protocol (at SIEMENS scanners) uses GRAPPA. However, only very few people pay a lot of attention on optimal usage of the GRAPPA auto-callibration data. I realized the importance of optimizing GRAPPA parameters when doing high-resolution EPI. At high resolutions, GRAPPA-related noise can become an increasingly important limitation.  This is especially true with the low bandwidth that the body gradient coils force us to use.

In this blog-post I will explain how the GRAPPA kernel-size affects the fMRI data quality, how you can change it, how you can find out which kernel-size was used, and I will descrive simple software tools to identify regions that might benefit from adaptations of the GRAPPA-kernel size.

Continue reading “GRAPPA kernel size”