Equi-voluming: The Anakin Skywalker of layering algorithms

Authors: Renzo Huber and Faruk Gulban

When you want to analyze functional magnetic resonance imaging (fMRI) signals across cortical depths, you need to know which voxel overlaps with which cortical depth. The relative cortical depth of each voxel is calculated based on the geometry of the proximal cortical gray matter boundaries. One of these boundaries is the inner gray matter boundary which often faces the white matter and the other boundary is the outer gray matter boundary which often faces the cerebrospinal fluid. Once the cortical depth of each voxel is calculated based on the cortical gray matter geometry, corresponding layers can be assigned to cortical depths based on several principles.

One of the fundamental principles used for “assigning layers to cortical depths” (aka layering, layerification) is the equi-volume principle. This layering principle was proposed by Bok in 1929, where he tries to subdivide the cortex across little layer-chunks that have the same volume. I.e. gyri and sulci will exhibit any given layer at a different cortical depth, dependent on the cortical folding and volume sizes (see figure below).

With respect to applying equi-volume principle in layer-fMRI, the equi-volume layering has gone through quite a story. A plot with many parallels to Anakin Skywalker.

In this blog, the equi-volume layering approach is evaluated. Furthermore, it is demonstrated how to use it in LAYNII software.

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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:

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Example analysis pipeline of layer-VASO

In this blog post I want to go through the analysis pipeline of layer-dependent VASO.

I will go through the all the analysis steps that need to be done to go from raw data from the scanner to final layer profiles. The entire thing will take about 30 min (10 min analysis and 20 min explaining and browsing through data).

During the entire analysis pipeline I am using the following software packages: SPM, AFNI, and LAYNII, and gnuplot (if you want fancier plotting tools)

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How many layers should I extract?

In this blog post, I want to share my thoughts on the number of layers that should be extracted from any given dataset. I will try to give an overview of how many layers are usually extracted in the field, I’ll describe my personal choices of layer numbers, and I will try to discuss the challenges of layer signal extraction along the way.

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Registration of high-resolution data

In this blog post Sri Kashyap and I describe how to deal with the registration of high-resolution datasets across days, across different resolutions, and across different sequences.

I am particularly fond of the following two tools: Firstly, ITK-SNAP for visually-guided manual alignment and secondly, using ANTs programs: antsRegistration and antsApplyTransforms.

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