Layer-fMRI Analysis Project 2025

Conducted in October 13-14th 2025

Coordinator: Jonathan Polimeni, Renzo Huber, and Luca Vizioli

Training Faculty: Laurentius Huber, Rainer Goebel, Anna Izabella Blazejewska, Luca Vizioli, and Jonathan Polimeni

One dataset, many analyses: an overview of the diverse processing approaches in layer-fMRI.

The layer-dinner group would like to invite you to show us your analysis pipeline in a brief presentation at an upcoming “Layer-fMRI dinner” in the Spring of 2022. The analysis of layer-fMRI data is challenging and not straightforwardly doable with standardized streamlines analysis packages. Most layer-fMRI groups have their own dedicated analysis solutions to account for layer-specific challenges. As such, the purpose of this event is:

To illustrate multiple layer analyses of members of the field, and for others to follow.
To highlight challenges of high-res and layer specific analysis.
To stimulate discussion about analysis challenges and solutions.
To give analysis developers a platform to advertise their analysis solutions.
To illustrate differences and similarities of pipelines.

Introduction by Jonathan Polimeni

Rainer Goebel: Brain Voyager

Lecture

Hands on

Renzo Huber: LayNii & AFNI

Lecture

Hands on:

Anna Blazejewska: Freesurfer

Lecture

Hand on instructions

For the BrainVoyager hands-on session by Rainer Goebel:

Please download the free educational version of BrainVoyager here (links will work shortly): For macOS (Apple Silicon ‘M’ chips): http://download.brainvoyager.com/temp/layer-fmri-course-cmrr/BrainVoyager_EDU_24.2-b2_arm64_Installer.pkg
For Windows users (or Mac users that want not to update to the new ‘b2’ version, they should download and unzip the following file: https://download.brainvoyager.com/temp/layer-fmri-course-cmrr/Layer-fMRI-Course-CMRR-2025-data-reg-update.bin.zip
All users should also download the following zip files with intermediate data files if possible:
https://download.brainvoyager.com/temp/layer-fmri-course-cmrr/Prepared-Anatomical-Files.zip
https://download.brainvoyager.com/temp/layer-fmri-course-cmrr/sub-demo_Avg-4runs-03-to-06_bold_AP_undist.zip
https://download.brainvoyager.com/temp/layer-fmri-course-cmrr/Coreg-files.zip
https://download.brainvoyager.com/temp/layer-fmri-course-cmrr/sub-demo_MP2RAGE_UNI_defaced_reframed_tissue-probs-slow.vmp.zip

For the LayNii-Afnii hands-on session by Renzo Huber, please download and install the following programs:

LayNii: https://github.com/layerfMRI/LAYNII and https://github.com/layerfMRI/LAYNII/tree/master/ida
AFNI binaries: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/download_links.html
ITK-snap: https://www.itksnap.org/

For the FreeSurfer hands-on session by Anna Blazajewska, there are no prior preparations needed. You will get server access. You can access the server with a vnc viewer.

Mac users can use the native VNC client.
Windows users will need to install a client such as TightVNC Viewer (https://www.tightvnc.com).
Instructions on how to use it are here.

The data that we will work with are below: