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 (email@example.com).
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: http://juhasilvanto.wordpress.com/ )'
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
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.
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
Retinotopic mapping with multifocal and block designs
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) []
And related literature[]
Color calibration, measured 11.9.2006.
Py luminances [cd/m2] for red, green and blue (at the moment these color calibration data are outdated)
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)