Vision Systems Neuroscience

Welcome to the home page of Vision Systems Neuroscience group. The group comprises two subgroups, Vision Systems Physiology and Visual Cognition and Awareness, who work in close collaboration. We are part of the Brain Research Unit of O.V. Lounasmaa Laboratory, and located in the Advanced Magnetic Imaging Centre at the Otaniemi campus of Aalto University in Espoo, Finland.

In the fall 2013, Simo Vanni relocated to University of Helsinki (



Vision Systems Physiology group

Simo Vanni, MD, PhD, Adjunct Professor (docent) at Helsinki University, Group Leader, Vision Systems Physiology group

Hanna Heikkinen, PhD, postdoc

Fariba Sharifian, MSc researcher, PhD student

Visual Cognition and Awareness Group

('Group website: )'

Juha Silvanto, PhD, Senior Scientist and Group Leader; Adjunct Professor at Dept of Psychology, Helsinki University

Anna-Maria Bique, PhD student

Silvia Bona, PhD student

Elyana Saad, PhD student

Contact Information

Brain Research Unit, O.V. Lounasmaa Laboratory at AMI Centre

Aalto University School of Science

Street address: Otakaari 5 I, Magnet House, 2nd floor

00076 Aalto, Finland

Postal address: P.O Box 13000, FI-00076 AALTO, Finland

Tel: + 358 - 50 437 1585 (Vanni)

Fax: +358 - 9 - 470 22969

Research Interests, Collaboration and Publications

About thirty distinct functional areas in each hemisphere participate in vision, covering more than 25% of human cortex. Routing of information in this system is dynamic and processing effective. We are studying the early phase of visual processing and hope to better understand the relation between measured imaging signals, visual behaviour, and biological image analysis. We also hope to distribute knowledge to clinicians and help development of mechanical applications of vision.

Vision Systems Physiology: Projects

Vision Systems Physiology: Collaborators

Vision Systems Physiology: Publications

Vision Systems Physiology: Stimuli

Vision Systems Neuroscience: Journal Club

Visual cognition and awareness: Projects

Visual cognition and awareness: Collaborators

Visual cognition and awareness: Publications


fMRI school 2013 A two-day course (17.-18.9.2013) on the basics of fMRI

fMRI school 2012 A two-day course (3.-4.5.2012) on the basics of fMRI

fMRI school 2011 A two-day course (4.-5.4.2011) on the basics of fMRI

fMRI school 2009 A two-day course (27.-28.10.2009) on the basics of fMRI


Voxel surround suppression model - 2012

A model for surround suppression in a single fMRI voxel, in which all parameters are strictly constrained by experimental data.

Matlab implementation of voxel area summation model - 2009

We have developed an area summation model for a single voxel in the human V1. The model consists of units with the same receptive field structure than in single neurons in macaque V1. The model contains no free parameters and still produces a reasonable fit to human area summation data. Please unzip the package to your directory and see voxel_area_summation_model.m for further instructions on how to use the program.

SPM and Freesurfer

Script reads Analyze volume to workspace and plots corresponding histogram: image_histogram.m

Function converts matlab 7 .mat files to matlab 6 readable format. The hdr and img files do not need conversion. Use from matlab 7: convert_v7v6.m

Batch script for fMRI data preprocessing (includes slice timing correction, realignment and smoothing): BatchExample_sli_rea_linda_1550.m

Batch script for fMRI data preprocessing for SKYRA (includes format conversion, slice timing correction, realignment and smoothing): conv_sli_rea_SKYRA_example.m. You need also spm_visionS_dicom.m and spm_visionS_dicom_convert.m in your path.

‎Slides for SPM driving school course: SPMdschool

Script for launching other scripts or functions at desired time: timer_simple.m

ROI selection and plotting for spm: spm_image

Average freesurfer overlay: How to & morph, conversion to ascii & final conversion from ascii to curv. Average m-file for Matlab

SPM8 upgrade

Retinotopic mapping with multifocal and block designs

Mapping instructions

Reference: Henriksson L, Karvonen J, Salminen-Vaparanta N, Railo H, and Vanni S. Retinotopic Maps, Spatial Tuning, and Locations of Human Visual Areas in Surface Coordinates Characterized with Multifocal and Blocked fMRI Designs. PLoS ONE, 7(5): e36859, 2012. doi:10.1371/journal.pone.0036859.

Calibration of AMI visual projection system & other technical information

Below you can find information on our luminancemeter calibration.

FMRI data projector's lamp was changed 28.6.2013.

Stimulus-PC was replaced 12.11.2009.

FMRI data projector gray-scale luminance output values were measured 1.07.2013 with the XP Windows stimulus PC.





Matlab implementation of BRS, an event-related fMRI model (beta - no warranty of quality) [[1]]

And related literature[[2]]

Guide for eye-tracking in AMI centre

Color calibration, measured 11.9.2006.

Py luminances [cd/m2] for red, green and blue (at the moment these color calibration data are outdated)

gammaR.dat, gammaG.dat, gammaB.dat

Py, Rx and Bz measurements in [cd/m2] for red (255,0,0), green (0,255,0) and blue (0,0,255) (at the moment these color calibration data are outdated)

chromaR.dat, chromaG.dat, chromaB.dat