Negative Voxels in VASO

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.

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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”

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.

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