Meeting minutes of the virtual layer-fMRI event #1

On May 7th 2020, there was a virtual layerfMRI event to discuss current issues in the field.

This meeting was held as a replacement of an originally planned layer-fMRI dinner at ISMRM and happened in succession of an earlier in-person layerfMRI workshop in November 2019 (meeting minutes here).

Below you find the important links of the the virtual event, videos of the talks and discussions, and a summary of the hot topics that were discussed.

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MP2RAGE: challenges and artifacts of its use for layer-fMRI

The MP2RAGE sequence is very popular for 7T anatomical imaging and is very commonly used to acquire 0.7-1 mm resolution whole brain anatomical reference data. Aside of this common application, it can also be very helpful for layer-fMRI studies to obtain even higher resolution T1 maps in the range of 0.5mm iso. However, when optimizing MP2RAGE sequence parameters for layer-fMRI studies, there are a few things that might be helpful to keep in mind.

In this post, I would like to discuss the challenges of using the popular MP2RAGE sequence in layer-fMRI studies. Specifically I will discuss challenges/features regarding:

Continue reading “MP2RAGE: challenges and artifacts of its use for layer-fMRI”

Quick example of cortical unfolding in LAYNII

Update June 2021: There is a new and more comprehensive 3D-supported LayNii Program for cortical unfolding. Please see

The blog post below is kept for archiving purposes: 

In this Blog post, I seek to describe a quick example of how to analyse high-resolution data across layers and columns with LAYNII.

Continue reading “Quick example of cortical unfolding in LAYNII”

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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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”