In the last years, I and multiple other VASO users have encountered many occasions of voxels that show negative CBV change (positive VASO signal change) while the BOLD suggests that the activation should be positive. In this blog post, I want to list potential sources of this surprising effect.
How send raw k-space data to any given server with Twix or with a modified ICE-chain
In this blog-post I want to describe a setup, how you can include an additional ICE functor in your reconstruction pipeline that sends raw Twix files from the Reconstruction computer to any given custom server. Continue reading “How send raw k-space data to any given server with Twix or with a modified ICE-chain”
How to install nifty QuickLook
In this blogpost I describe how to install a Quicklook plugin for nii files for mac OS. Continue reading “How to install nifty QuickLook”
3D-printing nii data
In this blog post, I want to write about pipelines on how to prepare Nifti-brain data and make them printable by a 3D-printer.
Two pipelines are shown. One pipeline describes the 3D-printing the cortical folding structure that is estimated with Freesurfer and subsequently corrected with Meshlab. And another pipeline describes how you can 3D-print any binary nii-volume by using the AFNI-program IsoSurface and correct the output with netfabb. Continue reading “3D-printing nii data”
How to convert any paper figure into a layer-profile
Often we would like to normalize depth-dependent fMRI signals and assign it to specific cytoarchitectonially defined cortical layers. However, we often only have access to cytoarchitectonial histology data in the form to figures in papers. But since we only have the web-view or the PDF available, we cannot easily extract those data as a layer-profile. Since most layering tools are designed for nii data only, paper figures (e.g. jpg or GNP) are not straight-forwardly transformed to layer profiles.
In this blob post, I describe a set of steps on how to convert any paper figure into a nii-file that allows the extraction of layer profiles.
Continue reading “How to convert any paper figure into a layer-profile”
GRAPPA regularization
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.
layer-fMRI abstracts at ISMRM and OHBM 2018
The following is a personal selection of my must-see layer-fMRI abstracts presented at ISMRM and OHBM in 2018. If I missed something, please let me know.
Continue reading “layer-fMRI abstracts at ISMRM and OHBM 2018”
