AMI Centre facilities - IT systems

AMI network in a nutshell

AMI Centre has its own internal network separated from the WWW by the Aalto University firewall and AMI Centre's own firewall. The strict firewall policy is needed because of the nature and amount of subject/medical data in our network. The network backbone consists of two servers: AMIserver and Langara, both of which provide basic network services. Servers have a disk array for home-directories of the users (backed-up) and work disk for temporary data analysis purposes (not backed-up). In addition to these, the server Langara has 32 GB of memory for those users who need to do memory intensive computer operations. All AMI users who need to transfer data, analyse data locally at AMI, are visitors, sit permanently in the premises of AMI Centre (Magnethouse, Otakaari 5 I) or who are otherwise justified to having user rights to the network will be granted these rights. In order to get your user account, please contact AMI Centre personnel.

AMI workstations are connected to AMI internal network and have a direct access to AMIserver, Langara, and the web services, such as printing and WWW. The workstations should be provided/paid by the individual group that you work with, but AMI IT-support personnel will help you in determining the composition of the desktop computer (either Linux or Windows is supported). The data disks on the workstations are not backed-up, so you need to take care of backing-up your data by yourself! Only the home directories in the AMIserver are backed-up, but because there is a strict quota on the amount of data you can store in your home directory, do not even try saving any imaging data to your home directory. Therefore, use your own local media for storing imaging data. Please note, that you can connect your own laptop to our guest network without the AMI user account in order to use basic web services.

Figure 1. Illustration of AMI Centre network infrastructure.

Image transfer and grace period

When you perform MR scanning at the magnet console, your image data will automatically be transferred to AMIserver's /opt/dicom_images/sorted/<Referring_Physician> -folder based on the name you provide to the field "Referring physician" at the magnet console. If you leave the field blank, the data will be transferred to a folder named "Unknown_referring_physician". From there onwards, there are several ways how you can transfer your data to your desired location:

  1. You can use secure copy (ssh/scp) in AMI network to copy data to your desired location (outside network). Please note, that you cannot connect with ssh to AMI Centre directly from outside due to our strict firewall, so you have to do this from inside AMI Centre. The data is kept in AMIserver for at least two weeks after which it can be removed from AMIserver without further notice.
  2. If you sit permanently at Magnethouse and you have a Linux workstation, we can configure your data to be automatically transferred to your own desktop's /opt/dicom_images/ -folder. In addition, the data is kept in AMIserver for at least two weeks after which it can be removed from AMIserver without further notice. Before the end of this grace period, you must verify that your data has been transferred to your local workstation!
  3. You can save the data directly to CD/DVD at the magnet console. (The data is still kept in AMIserver for at least two weeks.) On the magnet console, the data is removed in the oldest-first order when the console computer's hard drive is filling up. In normal usage, this means that the data will stay 1-2 weeks on the console before removed.

In all cases, please note that AMI Centre only guarantees that your data will stay in AMIserver for two weeks! After this grace period, it may be removed without further notice, so move/copy and back-up your data as soon as possible after you have finished scanning to make sure that you will have your data. Also, when performing data transfer, please verify that your data has actually been transferred to your remote location.

Remote use of AMI workstations

AMI Centre offers an option for remote access of AMI workstations. Service opens up a remote possibility to transfer data and to run processes that requires large amount of memory. The remote access is possible with Windows, Mac OSX or Linux operating systems. If you have an AMI account and you would like to use this service, please contact Tuomas Tolvanen ([email protected]) for detailed instructions and scripts.


Figure 1. Illustration of remote access at AMI Centre.

Stimulus and other computers

Please note that all stimulus computers are not (actively) backed-up, so you must have your own back-ups for your Presentation scripts and stimuli. Also, when measuring EEG, eye-movement etc. you should copy/move your data to your own preferred media as soon as possible, because those computers are used by several different people and the data is not backed-up either. It is possible that someone else might accidentally delete/overwrite your data, a hard-drive failure might occur and so on.

Supported software

Installed software for data analysis and stimulus delivery.

AMI Centre provides installations for data analysis software used by fMRI researchers working in AMI Centre. Due to several researchers performing their data analysis in the same campus, the knowhow on the following software is extensive and they are also available to users working inside AMI Centre's computer network:

  • MATLAB (under Aalto University campus license)
  • FreeSurfer
  • SPM (several versions; 2, 5, and 8)
  • FSL
  • BrainVoyager
  • BrainProducts' Analyzer

For stimulus delivery, the following software are supported by AMI Centre:

  • Presentation (newest, and one or two previous releases)
  • E-Prime
  • (Psychtoolbox)

Aalto NeuroImaging Infrastructure

ANI research infrastructure houses four functional neuroimaging modalities, navigated transcranial magnetic stimulation (nTMS) at Aalto TMS, functional magnetic resonance imaging (fMRI) at Advanced Magnetic Imaging (AMI) Centre, magnetoencephalography (MEG) at MEG Core and Aalto Behavioral Laboratory (ABL).

Aalto Behavioral Laboratory

Aalto Behavioral Laboratory

Aalto Behavioral Laboratory (ABL) has various different monitoring and stimulus systems for behavioral studies in controlled environment. The laboratory consists of two measurement rooms: a shielded room which is especially intended for EEG and remote eye tracking measurements; and a room for behavioral measurements which doesn’t require shielded conditions.

Aalto TMS

Aalto Transcranial Magnetic Stimulation

Aalto TMS offers researchers unique possibilities for multi-modal neuroimaging techniques. The laboratory contains top-of-the-line electroencelography (EEG) and transcranial magnetic stimulation (TMS) systems.

Magnetoencephalography (MEG)

MEG Core

MEG Core offers excellent environment for MEG measurements. MEG Core has a modern 306-channel MEG device (Elekta Neuromag™, Elekta Oy, Helsinki, Finland) in a high-end 3-layered magneticaly shielded roo (Imedco AG, Hägendorf, Switzerland). MEG Core has extremely low magnetic ambient noise level. MEG Core has a wide variety of MEG-compatible stimulators and monitoring devices.

This service is provided by:

Aalto NeuroImaging Infrastructure

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