Partial-Fourier imaging at High Resolutions

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.

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Smoothing within layers

Smoothing within layers can be advantageous for multiple reasons:

  • Increasing the CNR without loosing spatial information across cortical depths.
  • Visualization of striping pattern across columnar structures.
  • Avoiding leakage of physiological noise from CSF space into GM tissue.

image88.gif Continue reading “Smoothing within layers”

Finding ROI of the double layers in M1

In this post I want to describe the guidelines that helped me to find the right spot of primary motor cortex (M1) that has a double-layer pattern during a conventional finger tapping task.

The motor cortex is an excellent model system to debug-layer fMRI methodology for multiple reasons:

  1. It has a consistent folding pattern across people.
  2. Its folding pattern is convoluted across one axis only. Hence, it is possible to use thicker slices with higher in-plane resolution.
  3. With 4mm, its is the thickest part of the cortex compared to all other areas. Hence, layer analysis can be done even with 1.2 mm voxels.
  4. It has an expected double layer structure, with two separate peaks. The separability of the peaks can be used as a measure of functional specificity.
  5. It is very close to the RF-receive coils and has high tSNR.
  6. It is easy to shim.

One tricky part, however, is to find the right location of the double layer feature.

Continue reading “Finding ROI of the double layers in M1”

Quick analysis pipeline of getting layer fMRI profiles without anatomical reference data

This is a step-by-step description on how to obtain layer profiles from any high-resolution fMRI dataset. It is based on manual delineated ROIs and does not require the tricky analysis steps including distortion correction, registration to whole brain “anatomical” datasets, or automatic tissue type segmentation. Hence this is a very quick way for a first glance of the freshly acquired data.

This post shows how you can get from activation maps to layer-profiles in 10 min. In a quick and dirty way.

The important steps are: 1.) Upscaling, 2.) Manual delineation of GM, 3.) Calculation of cortical depths in ROI, 4.) Extracting functional data based on calculated cortical depths.

Continue reading “Quick analysis pipeline of getting layer fMRI profiles without anatomical reference data”

Gradient Temperature

tSNR changes across time

I got interested in gradient temperature because of the weird effect that tSNR seemed to increase over time.

Upon posing this effect on Twitter, PracitalfMRI and Ben Poser suggested that it might be due to gradient temperature. So I learned how to track it with as described below.

Continue reading “Gradient Temperature”

GRAPPA kernel size

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.

Continue reading “GRAPPA kernel size”

layer-fMRI software repositories

There is a long list of software packages that are capable of performing high-resolution MRI analysis.

Some of them are used by multiple groups and some of them are customized for specific studies only.

In this post, I want to give an overview over the most important software packages, their advantages and disadvantages, and their popularity in the field.

Continue reading “layer-fMRI software repositories”

Layer fMRI papers

This page depicts a collection of all layer-fMRI papers.

This list only includes papers that focus on: cortical layer-fMRI in humans. Preprints are included.
Suggestions are welcome

For non-cortical, non-fMRI, non-human, or non-layer high resolution MRI, please see reviews in special issues 1, 2, 3 (and references therein).

Screenshot 2021-02-11 at 12.22.37

A mirrored full list can be found here.
















Bias field correction

This post shows the overview of doing bias field correction in in SPM. Doing this helps me a lot to improve the accuracy of FreeSurfer with MP2RAGE data. The members of Polimeni’s group also use it as an additional per-processing step before giving the data to Freesurfer.

The SPM bis field correction is part of the segmentation pipeline in SPM. I use the following bash script and the following matlab stript:

Bias_field_script_job.m and

Continue reading “Bias field correction”

Using a standalone Nifti I/O in C++

In this blog post, I describe how you can build your own standalone C++ program to analyze nii data without any dependencies beyond C++.  Hence, it will work without the  libraries from other fMRI software packages, e.g. odin, afni. The only tricky part is to use a stand alone nii I/O to write your own C++ evaluation programs. Here, I do it by incorporating the few files that i borrowed from the afni source code.

Continue reading “Using a standalone Nifti I/O in C++”

How to deal with Ghosts in high-res EPI


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.

Continue reading “How to deal with Ghosts in high-res EPI”

Getting layers in EPI space


Big steps:

  1. Manual aligment of MP2RAGE with EPI (optional when MP2RAGE is acquired in same session)
  2. ANTS alignment of MP2RAGE and EPI. (part of, see github)
  3. Running Freesurfer on MP2RAGE data in EPI space. (part of, see github)
  4. Using SUMA to get fine samples tissue borders in EPI-voxel space (in oblique space) (part of, see github)
  5. Manual correction of Freesurfer GM-ribbon
  6. calculating layers from GM-ribbon in neuroDebian.

Continue reading “Getting layers in EPI space”

Motion and BOLD correction in SS-SI-VASO


This is a description on how to use SPM and/or AFNI for high-resolution SS-SI-VASO data evaluations.

Here it is explained what to do with the raw fMTR data from the scanner to obtain CBV and BOLD signal time courses .


Every other image has a different contrast.

Screenshot 2017-11-25 15.27.14.png

Continue reading “Motion and BOLD correction in SS-SI-VASO”

brain art

This is a collection of brain art that I made.

2020 Candy brain, generated with LAYNII’s LN2_COLUMNS from Faruk Omer Gulban

2020 challenge by OHBM


2020: The Australians die equi-distant layers long before is was cool: Aboriginal art in LAYINII.


2020: The brain as seen from a precessing proton.

2020: Feeling lost in the hunt for resolution. Nothing will ever be high enough


2019: pulsed source

2019: Verzwirbelter Zwirn II


2019: spectral brain


2019: brain shape in in the style of a Cajal drawing of a Purkinje Cell

2018: broken phone screen edited with deep-learning algorithm


2019: MRI fireworks with broccoli


2018: Never ending layers


2018: Joy of layering (based on idea from Erika Raven)

The profiles refer to myelin stain profiles of multiple brain areas. The thickest one it from motor cortex and the thinnest one is from sensory cortex. The y-axis refers to gray values of drawings from Theodor Kaehs.


2018: The devils brain (3D print, painted with nail polish)


2018: The horned brain


2018: the exploding brain (when the cortical smoothing algorithm is buggy)


2018: The firing brain


2018: Physiological noise




2018: You are your brain and your brain is us (Wax on plastic)



2018: Layer T-shirt

Screenshot 2018-01-27 11.05.46.png

2018: growing layers


2018: surfaces on volume


2018 I am my brain and my brain is me


2017 flow mapping in DC (the voxel state)


2017 Weapon of choice


2016 Fingerprinting


2016 Fractal wax


2017 Brain storming


2017 Cajal


2017 Weapon of choice and fractal brain tree


2015: Bark


2015: Brain roots


2016: Origami


2015: Zwirbelnder Zwirn


2016: Brain ball (Franklin Institute gift shop)


2016: HAWAII: Surfing the surfaces


2016: Aborigines: They did equi-distant long before it was cool


2015: paper


2016: Future planning insecurity problems of foreign post doc in neuroscience: politics and money