Vascular Space Occupancy is an fMRI method that is popular for high-resolution layer-fMRI. Currently, the most popular sequence is the one by Rüdiger Stirnberg from the DZNE in Bonn, which is actively being employed at more than 30 sites.
This sequence concomitantly acquires fMRI BOLD and blood volume signals. In the SIEMENS reconstruction pipeline, these signals are mixed together within the same time series, which challenges its user friendliness. Specifically: The “raw” dicom2nii-converted time-series are not BIDS compatible (see https://github.com/bids-standard/bids-specification/issues/1001). The order of odd and even BOLD and VASO image TRs is dependent on the nii-converter. Workarounds with 3D distortion correction, results in interpolation artifacts. Workarounds without MOSAIC decorators result in impracticable large data sizes.
The goal of this Hackathon is to extend the 3D-MOSAIC to solve these constraints. This functor is commonly used to sort images by echo-times, by RF-channels, by magnitude and phase in the SIEMENS reconstruction pipeline into sets of mosaics . However currently, this functor does not yet support the dimensionality of SETs. In this project we seek to include SETs into the capabilities of the functor.
This page describes the use of a VASO sequence for SIEMENS scanners with the software platform VE. This sequence uses a 3D-EPI readout and is written by Rüdiger (Rüdi) Stirnberg and Tony Stöcker (DZNE, Bonn).
Are you ever annoyed how hard it is to get brain data off the scanner? The fact that scanners usually contain private information about patients and are thus embedded in maximally restrictive clinical cyber-security environments, makes it quite complicated to get access to the data. Especially when visiting collaborative sites.
In this this Hackathon project, we aim to develop a purely uni-directional (safe) data streaming “hack” to transfer MRI data directly to the cloud by means dynamic QR codes.
In the early days of the Internet, modems (modulator-demodulator) were used to (i) convert digital information into audio streams, (ii) transfer them across telephone lines, and (iii) convert them back into the digital domain. Here, we aim to do the same thing with pixel data of MRI scans. However, instead of audio signal we will use machine-readable visual information: QR codes.
Specific aims of the Brain QR modem
1.) We will develop an ICE-Functor that converts pixel data to QR codes in real time
2.) We will develop an Android app that converts the streamed QR coded into a series of png that are directly streamed to the cloud (Drive folder).
3.) We will develop a LayNii program that converts stacks of PNG images into Nii files.
This project contains many consecutive components of a modem. And will likely take 2-3 rounds of Hackathons to be completed.
This blog post represents a continuation of the manuals regarding VASO acquisition and VASO signal analysis. It deals with the question of quantifying the VASO signal change with respect to the baseline blood volume at rest. In this post, I try to provide an overview of the values of baseline blood volume in the literature, I hypothesise reasons for their discrepancy and conclude by arguing that one should refrain from analyzing VASO in relative units after all.
Title: High resolution fMRI: An introductory course for data acquisition and analysis challenges.
Support: This lecture series is finanzially supported by the FPN-MBIC-school. The session on sequences and sequence artifacts is supported (in kind) by the York-Maastricht-partnership grant. Faruk Omer Gulban works for Brain Innovation.
Coordinators: Laurentius (Renzo) Huber & Omer Faruk Gulban, Cognitive Neuroscience Department
CBV-fMRI with VASO is highly dependent on a good inversion contrast. It gives it its CBV sensitivity and is also responsible for most of the VASO specific pitfalls (e.g. inflow, CSF etc. ). And thus, it should be optimized as much as possible.
In this blog post, I want to describe the most important features of a reliable inversion pulse for the application of VASO at 7T with a head transmit coil.
In this blog post I want to discuss how the tSNR in sub-millimeter fMRI can be substantially improved by optimizing the GRAPPA regularization. Adjusting one single GRAPPA reconstruction parameter can almost double the tSNR of your fMRI time series. With almost no penalty.
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
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
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.
With respect to high-resolution VASO application, visual cortex is very unique. I found it to be a challenging area. However, because of its high demand, I have been working on is with multiple collaborators. The most important pitfalls of SS-SI VASO in visual cortex that I came across in these collaborations are discussed below.
The take home message tat I learned from manny experiments is:
Use axial slices with the phase encoding direction A>>P.
Watch out for negative voxels.
Invest a lot of effort in optimizing GRAPPA parameters, its worth it.
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.
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.
Ghost are the biggest limitation in high res fMRI. Similar to low resolution fMRI, ghosts in sub-millimeter EPI are arising from mismatch of k-space lines. This mismatch can be associated with (A) the actual readout itself or (B) inappropriate GRAPPA auto calibration data.
Here I try to make notes of strategies that I found helpful to minimize ghosts.