BRAIN RESEARCH UNIT

A Visitor's Guide

Jaakko Järvinen

Brain Research UnitLow Temperature Laboratory

Helsinki University of Technology

Spring 2000

TABLE OF CONTENTS

Introduction ..................................................................................................................... 11. Surviving in the Brain Research Unit ......................................................................... 2

Anatomy of the Brain Research Unit .................................................................. 2Arriving at Low Temperature Laboratory .......................................................... 3Buses and timetables ........................................................................................... 3Monkey board ..................................................................................................... 4Where to go for lunch?........................................................................................ 4Coffee break ........................................................................................................ 5Ice cream, sweets, and drinks.............................................................................. 6Shower room ....................................................................................................... 6Journals and books .............................................................................................. 6Reprint collection ................................................................................................ 7Photocopier ......................................................................................................... 7Office equipment................................................................................................. 7Services in Otaniemi ........................................................................................... 8Monday meeting ................................................................................................. 8Magnetic resonance images ................................................................................ 8Flow of information ............................................................................................ 9

Mailing lists............................................................................................. 9Home page .............................................................................................. 9Notice boards .......................................................................................... 9Telephone ................................................................................................ 9Telefax .................................................................................................... 10Incoming and outgoing mail ................................................................... 10

Libraries .............................................................................................................. 10Library of Technical Physics .................................................................. 10National Resource Library for Technology ............................................ 10National Library of Health Sciences ....................................................... 11Helsinki University Library .................................................................... 11Viikki Science Library ............................................................................ 11

2. Using computers ......................................................................................................... 12Macintosh system................................................................................................ 12Printers ................................................................................................................ 12Scanner ................................................................................................................ 13UNIX environment ............................................................................................. 13Magneto-optical disks ......................................................................................... 15Saving evoked responses and raw data ............................................................... 16

3. Working in the measurement room............................................................................. 17Reserving a measurement time ........................................................................... 17Operating Vectorview ......................................................................................... 18Stimulation systems ............................................................................................ 18Magnetically shielded room................................................................................ 19

Protecting Vectorview from magnetic contamination ............................ 19Monitoring the subject ............................................................................ 19Forcing the door open ............................................................................. 20

Laboratory safety ................................................................................................ 20Moving the Vectorview probe unit ......................................................... 20Dealing with liquid helium ..................................................................... 21Keep an eye on the subject...................................................................... 21Fire, acute illness, or other serious emergency ....................................... 21

Sources of artefacts ............................................................................................. 21When leaving the measurement room................................................................. 22

4. Afterword .................................................................................................................... 23

1

Introduction

Welcome to the Brain Research Unit of Low Temperature Laboratory! I hope that you

enjoy the international, interdisciplinary and friendly atmosphere in this research

team. The symbolic animal of the Low Temperature Laboratory, the penguin, can be

seen marching on the cover.

Everybody is a visitor of some sort. Some visitors stay just for a couple of weeks,

others for the rest of their lives, but everyone of them has to survive the first few days.

This survival guide was written mainly for visitors and new employees, but also their

tutors may find this guide a useful reference. Still, nothing can replace a tutorial given

by an experienced lab member.

Adaptation to a new environment takes time. This guide is like a catalyst in the sense

that it should speed up the adaptation process. Furthermore, many things concerning

laboratory safety, laboratory practice and established customs can be learned easily

from this text. I welcome proposals for improving the guide and wish the reader a

pleasant stay in the Brain Research Unit of the Low Temperature Laboratory.

Jaakko Järvinen

Otaniemi, 14th February 2000

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1. Surviving in the Brain Research Unit

ANATOMY OF THE BRAIN RESEARCH UNIT

Brain Research Unit (BRU) is a part of Low Temperature Laboratory (LTL), which is

a part of Helsinki University of Technology (HUT). Our premises are located in

Otaniemi, Espoo, on the campus of HUT. The offices of BRU are all in the

Engineering Physics Building, but distributed to three different parts of it. The main

entrance is through staircase A in the address Otakaari 3. The yellow door of the new

MEG measurement room is the first thing you see when you come in.

The nucleus of all activity is the long corridor on the first floor. For example, all

secretaries' offices are along this corridor. Technical workshops of the lab start where

the corridor ends. Some BRU offices are on the third floor. Some people call the third

floor Tibet.

A satellite BRU office block that we call Siberia is located in the same building, but

in another staircase (H). The name Siberia is a black humour combination of the low

temperature that we are dealing with in LTL, and the historical fact that many Finnish

criminals were transported to the cold Siberia under the Russian regime 1809–1917...

Our postal address:

Brain Research Unit

Low Temperature Laboratory

P.O. Box 2200

02015 HUT, Espoo

Finland

Our visit address:

Low Temperature Laboratory

Otakaari 3 A

Espoo

Finland

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The home page of Low Temperature Laboratory is at http://boojum.hut.fi. The home

page of Helsinki University of Technology is at http://www.hut.fi.

ARRIVING AT LOW TEMPERATURE LABORATORY

One of the members of the laboratory will be named as your tutor, who will for

example give you a sight-seeing tour in the lab, and help you in getting an e-mail

account and the keys to the lab. The secretaries are happy to advise you in many

practical questions. Try to get familiar with as many people as possible right in the

beginning.

Your first hurdle here will be getting a login name and a password for the local UNIX

system. Ask for an e-mail account and that your name is added to the BRU's mailing

list, aivo@neuro.hut.fi (see also Flow of information: Mailing lists). One of the

superusers can help you with these (e.g. Dr. Matti Hämäläinen, Dr. Veikko Jousmäki

or Mr. Kimmo Uutela). Learn your password by heart and don't reveal it to any living

soul.

The secretaries will give you the keys that you will need: one black plastic key for

opening the fire doors, and one brass key for opening the office doors. The automatic

locks will close the fire doors at 4.00 p.m., so it will be hard to navigate in the lab

without keys after that time. The black plastic key will also open the front doors, and

it can be used as a time card. (You may be asked to sign yourself in every morning

and out every evening. Your tutor or Ms. Marja Holmström (office F146) will show

you how. Ask the secretaries if this concerns you, as the regulations may change.)

Please have a look at LTL's home page http://boojum.hut.fi and fill in the registration

form as soon as you know your new e-mail address and your office number.

BUSES AND TIMETABLES

A lot of buses coming from many directions stop at Otaniemi. The fastest bus

connection between the center of Helsinki and LTL is bus 102 that departs from the

main bus station of Helsinki, at platform 51. Note that 102T is 5–9 minutes slower

because it drives through Lauttasaari.

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You can buy a single ticket from the driver. It will cost 16 FIM. You can buy

considerably cheaper serial tickets and bus passes from kiosks (look for the blue sign

"R-kioski"). In Otaniemi, the closest R-kioski is at the shopping mall (see section

Services in Otaniemi). You can ask for your own copy of the timetable booklet at the

main bus station of Helsinki. Information about timetables can also be found at

http://www.ytv.fi.

MONKEY BOARD

Have you forgotten somebody's name but dare not ask anymore? Or do you have an

inverse problem, that is, you know somebody's name but can't associate it with a face?

To get over such embarrassing situations, look at the picture gallery next to the

photocopier. Everyone in LTL is there, in alphabetical order.

If your face is not yet on the board, please ask Dr. Peter Berglund in office F147 for a

photography session. All information shown on the board is based on what you have

claimed when registering in LTL's home page, so please register first at

http://boojum.hut.fi.

WHERE TO GO FOR LUNCH?

There are several student restaurants in Otaniemi. Usually they all have vegetarian

and healthy options. Price for a lunch is about 20–30 FIM. For a little extra you can

take bread and drinks. Water and salad are included in the normal price.

Undergraduate students pay only 12–15 FIM for the lunch, because the student prices

are subsidized. To get the discount, the students have to prove their student status by

showing a student card. This list of lunch restaurants is far from complete, but

includes the most popular choices among the lab staff:

KVARKKI (Otakaari 3, 2nd floor)

The nearest alternative, in the same house as the lab. For some reason, Riitta Hari

calls this place the cafeteria of spreading depression. Fresh coffeebread in the

morning.

SÄHKÖ I & II (Otakaari 5, 2nd floor)

The second closest alternative. Better opening hours than in Kvarkki.

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DIPOLI (Otakaari 24, 2nd floor)

The biggest variety.

SMÖKKI (Jämeräntaival 4)

Pizza baked on demand. Other plates are the same as in the previously mentioned

restaurants. Smökki, Dipoli, Sähkö and Kvarkki all belong to Sodexho restaurant

chain.

TÄFFÄ (Otakaari 22)

A restaurant owned by the Union of Swedish speaking students of technology.

COFFEE BREAK

Coffee consumption per capita in Finland is the biggest in the world. Only in Seattle

in U.S.A. do people drink comparable amounts of coffee. Every weekday at 2.00 p.m.

a bell rings and all scientific activity stops because of the coffee break. The gathering

spot is the long corridor on the first floor. This is a golden opportunity to meet your

colleagues and people from other, more physics-oriented research units of LTL, e.g.

INTERFACE, NANO, ROTA, and YKI.

Coffee machines are located on the first and third floors. If you need small coins to

buy coffee, go to Pirjo Kinanen's office (F146) to change money. The machine on the

first floor won't give any change, so be sure to insert the exact amount. Tea is

available during the coffee break (see the section Ice cream, sweets, and drinks for

paying the tea bill).

Sometimes free cakes or sweets are provided by someone who wants to celebrate a

grant, a prize, a marriage, a new baby, a birthday, or a successful defence of a doctoral

thesis. Any other reasons for offering cake, including no reason at all, are accepted. If

you wish to offer cake, ask the secretaries for advice.

Those people who have served LTL for more than two months, and are going to leave

LTL permanently, are invited as members to the Penguin Club. They are awarded a

small glass penguin as a souvenir. Usually the penguin is awarded in connection with

the coffee break on the last day when the person leaving LTL is at work. Also on this

occasion, it is customary that the new member of the Penguin Club provides some

cake.

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ICE CREAM, SWEETS, AND DRINKS

The continuity of scientific output is ensured also outside office hours: soft drinks, ice

cream and sweets are available at all times at a low cost. Ice cream is in a freezer at

the end of the first floor corridor. Sweets are on a bookshelf in office F146. Drinks are

in a fridge in office F138. You will find a list in close proximity of whatever you are

taking; please check if your name is on the list. If not, add your name on it. Then

mark every item that you have taken to the appropriate column. If you drink tea that is

served during the coffee break, please make sure that you mark yourself on the tea

drinkers' list, to either "daily" or "monthly" column. Ms. Pirjo Kinanen will collect the

money once a month. Please remember to pay your ice cream bill before it is

hundreds of FIMs, or, at the latest, before leaving the country.

SHOWER ROOM

It is possible to take a shower in the lab, which is a nice thing especially in the

summertime when people come to work by bike. The shower room and the cloak

room (F149) are on the first floor, next to the ice cream freezer. Please bring your

own towel, shampoo and conditioner. Use the two-sided sign (red side for female,

blue side for male) to indicate that you are inside by hanging the sign on the door.

Remember to remove the sign when leaving the room!

You can ask the secretaries if there are any free lockers in the cloakroom. Please

return the locker keys when you don't need them anymore, because there are more

potential users than there are lockers. In an emergency, e.g. if you missed the last bus,

you can sleep in the cloakroom bed. Close the window if it is open — we don't want

burglars here. Keep the cloakroom clean.

JOURNALS AND BOOKS

We receive some of the most important journals in the field of neuroscience to the lab.

The most recent issues are placed on the journal desk in the first floor corridor. Newly

purchased books are also placed on that desk for some time. If you take a book or a

journal to your room for longer than a few hours, please leave a message on the table

and send a note about this to the aivo mailing list. The same applies if you borrow

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books from somebody's office. Always ask first if you want to borrow somebody's

personal books or other items.

REPRINT COLLECTION

The most recent papers from LTL are exhibited for some time next to the coffee

machine on the first floor. You may not take these reprints for you, but read only. You

can get free reprints from the LTL archives. Reprints of all publications of LTL are

stored in the archives at the end of the first floor corridor. You may take reprints for

yourself, but don't take the last reprint — instead, copy it for yourself with the

photocopier.

PHOTOCOPIER

The photocopier in the middle of the first floor corridor works very quickly and

doesn't need a copycard to function, just dial the password 44444 and "enter". You

can save your time considerably by learning how to use some special features of this

machine. If you are making overhead transparencies, make sure that you use only

transparencies meant to be used in photocopiers. All other photocopiers inside or

outside HUT require a copycard, see Libraries. The lab has also a telefax machine,

see section Flow of information: Telefax .

OFFICE EQUIPMENT

Notebooks, pens, pencils, slide frames, folders, paper towels, Scotch tape, and other

office equipment can be found in the storeroom F133. If something is out of stock or

if you take the last item, you should inform the secretaries (office F146).

Computer equipment (MODs and ZIPs) can be found in Riitta Hari's office F143 on a

bookshelf, as well as DAT tapes, and film for colour slides. Normal 3.5'' diskettes can

be found in a side corridor, in a cupboard opposite to the office F164.

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SERVICES IN OTANIEMI

Close to the main building of the University of Technology, there is a tiny shopping

center including a bank (Merita), two automatic cash dispensers, a kiosk, a post office,

a pharmacy, a hot dog stand, and a couple of grocery stores. A small University

Bookstore (open Mon–Fri 9.00–16.30) is inside the main building of HUT. You will

find a much larger variety of shops and services in Tapiola, which is just five minutes

away by bus (buses 2, 4, 10, 15). Alternatively, try shopping malls in the center of

Helsinki for an even larger choice.

MONDAY MEETING

Members of the Brain Research Unit meet every Monday at 14.15 in the traditional

Monday seminar. There you will hear people presenting fresh MEG data, telling about

their experiences on conference trips and discussing hot topics of neuroscience.

Important announcements are given concerning laboratory practices and safety.

Sometimes we invite speakers from outside the lab to tell about their field of

expertise. "Barbecue" meetings are special occasions, where candidates for a Ph.D.

degree are grilled with hard questions a week or two before the public examination of

their Ph.D. dissertation. The idea of the barbecue is to constructively help the

candidate to find those weak points that he or she should still work on. Everyone is

encouraged to throw questions. The defence of the thesis should be a piece of cake

after the barbecue.

Usually the meeting is in the lecture theatre F1 or in the classroom F4. The topic and

place of the meeting are announced on the aivo mailing list, on LTL's home page

(http://boojum.hut.fi/seminars) and on the notice boards. All seminar presentations are

given in English. Every BRU member should participate in Monday meetings.

MAGNETIC RESONANCE IMAGES

If you are going to be a subject in MEG experiments, it is likely that magnetic

resonance images of your brain are needed to integrate the MEG information to your

personal anatomy. The images are taken at Helsinki University Hospital in Meilahti.

Our MRI contact person is MD Sari Avikainen (office F138). Please ask her about the

details.

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FLOW OF INFORMATION

Mailing lists

The main source of information about events in the lab is the mailing list

aivo@neuro.hut.fi ("aivo" is the Finnish word for brain). Be sure to join this mailing

list. Only the members of the Brain Research Unit read messages on it. There is

another mailing list, isoaivo@neuro.hut.fi ("isoaivo" meaning cerebrum), that is

read also by people who use the measurement room but are not necessarily members

of the lab. Use isoaivo list only when you have to make an announcement about

laboratory practice or safety. In all other cases use the internal aivo mailing list. To

send e-mail to all people on aivo mailing list, just send your e-mail message to the

address aivo@neuro.hut.fi. You can omit the "@neuro.hut.fi" if you are using the

UNIX system in the lab.

Home page

Low Temperature Laboratory has an informative home page whose address is

http://boojum.hut.fi/. All visitors and new employees of the lab should register by

filling in a form that can be found on this website. Please register as soon as possible

after you have arrived. You may also be interested in the home page of the Finnish

Brain Research Society, which can be found at http://boojum.hut.fi/brainsociety/.

Notice boards

In the first floor corridor, there are some notice boards worth watching. BRU's own

bulletin board is close to the laboratory entrance. There you will find announcements

about courses, scholarships, conferences and symposia. "Today" bulletin board

contains info about events on the same day.

Telephone

An updated telephone catalogue of the LTL is distributed to every office several times

a year. Please check that information about you is correct and let the secretaries know

if it isn't. When calling inside the University of Technology, just dial the four-digit

number, e.g. 2959 to Riitta Hari's office. If you are calling from outside the

University, add the prefix 451. Example: when calling Riitta Hari from the Helsinki-

Vantaa airport, dial 451 2959. If you phone from outside the capital region

(Helsinki/Espoo/Vantaa) in Finland, dial 09 451 2959. If you phone from abroad, dial

+ 358 9 451 2959 (the plus sign means the international call trunk prefix in your

country).

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If you make a telephone call from HUT to the outside world, dial 0 before any other

number. If calling abroad, use 999 as the international call trunk prefix — the

University has agreed with the teleoperator Finnet that only this prefix is used.

Example: when calling from HUT to number 234 5678 in Rome, Italy, dial 0 999 39

06 234 5678. However, it is not possible to call abroad from just any HUT telephone.

If you have to make an official telephone call, please ask the secretaries where you

can do it. See telephone catalogue for more information.

Telefax

The telefax number of LTL is + 358 - 9 - 451 2969. You'll find the fax machine in the

corridor next to Riitta Hari's office. Read the instructions before sending a telefax.

Incoming and outgoing mail

The incoming and outgoing mailboxes are located just outside office F146, in the first

floor corridor. From there, you can send mail in HUT's official prepaid envelopes

only. You can find these envelopes in the same place, on a shelf. If you are sending

personal mail, please take it to the post office at the Otaniemi shopping mall. Check

regularly whether there is mail for you in the incoming mailbox.

LIBRARIES

In this section, some of the most useful libraries are listed in the order of closeness,

starting with the nearest. For a more complete list of Finnish research libraries, see

http://hul.helsinki.fi/tilke/indexeng.html.

Library of Technical Physics

Otakaari 3A, Espoo. The librarian is present Mon–Fri 8.00–15.45, but you can visit

this library also outside office hours. This library is the nearest to the lab — it is

located in the same building on the second floor. It has a good collection of books and

journals about physics, but also some about neuroscience and biomagnetism. Note

that some older journals are stored in the basement. Take a copycard with you from

office F146 if you are planning to use the library's photocopier. See:

http://www.hut.fi/Units/Tf–library/.

National Resource Library for Technology

Otaniementie 9, Espoo. Open Mon–Fri 8.00–21.00, Sat 8.00–16.00. Tel. 451 4111. A

wealth of journals and books, in hard copy and on-line. See:

http://www.hut.fi/Units/Library/.

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National Library of Health Sciences

Haartmaninkatu 4, Helsinki. Open Mon–Fri 8.30–19.00, Sat 10.00–16.00. Tel. 191

26643. This library, which is located in the Helsinki University Central Hospital

region in Meilahti, has a very good journal collection in the field of health sciences,

including neuroscience. Bus 502 from Otakaari and buses 194 and 195 from the HUT

main building will take you there in 10–15 minutes.

The copying machines accept only the copycards of University of Helsinki. You may

take one such copycard with you from office F146 when you are going to Meilahti

library. You may have to buy a new copycard with your own money from the library.

However, the LTL secretaries will refund the price to you against the receipt and the

partly used copycard, if you have agreed with them about it beforehand.

Note: some journals are received only in an electrical form. Ask the librarians about

this. Observe that you can read e-journals and browse Medline and some other

databases also in LTL. For this, type http://www.terkko.helsinki.fi/english/

index.htm to your web browser. You need a login and a password to use these

services. BRU has its own login and password. You can ask anyone in the lab what

they are. You can browse Medline without any password at PubMed,

http://www4.ncbi.nlm.nih.gov/pubmed/medline.html. For more information,

contact Mr. Topi Tanskanen who is our e-journal contact person.

Helsinki University Library

Unioninkatu 36, Helsinki. Open Mon–Fri 9.00–20.00, Sat 9.00–16.00. Tel. 191

23196. This library is the Finnish national library and even if you don't need any

journals from its collections, it is worth seeing because of its architectural merits. For

example, note the famous galeria rotunda. Copycards of the University of Helsinki

are accepted and sold here, just like in Meilahti. For more information, see

http://hul.helsinki.fi/hyk/hul/indexe.html.

Viikki Science Library

Viikinkaari 11 A, Helsinki. Open Mon–Fri 9.00–18.00. Tel. 191 58026. Viikki

Science Library was opened in August 1999 and it is located in the Biocentre of

Viikki, the new campus of the University of Helsinki dedicated to research in

Biosciences. You can get there by bus, but you have to transfer and it may take an

hour. Some neurobiological journals come only to this library, which is specialized in

natural sciences. The same copycards as in the National Library of Health Sciences

and Helsinki University Library are accepted here. For more information, see

http://helix.helsinki.fi/infokeskus/lib/index.htm.

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2. Using computers

In the Brain Research Unit, we use HP-UNIX computers for handling MEG data and

Macintosh computers for writing, designing figures, and statistical analysis. We only

have a few PCs, whose operating system is Microsoft Windows. This chapter is not

intended to be a complete manual to using computers, but a short description of our

computing possibilities. Your tutor should help you in getting started, but at some

stage you have to pick up the manual yourself.

MACINTOSH SYSTEM

All of our Macs, UNIXes and printers are linked to each other via an Ethernet

network. It is possible to move files between computers through the net without any

involvement of diskettes. If you are planning to bring your own computer to the lab,

and would like to connect it to the net, your computer should have a twisted pair or a

thin ethernet connector. Furthermore, you will need an IP address, which Dr. Veikko

Jousmäki (office F345) can make for you.

Some of our commonly used software for Macintosh include Microsoft Word,

EndNote, Microsoft Excel, Adobe Photoshop, Adobe Illustrator, Stat-view, F-Secure

SSH, Fetch, and Netscape. Manuals to many of these software are available in Dr.

Peter Berglund's office (F147) or in one of the cupboards in a side corridor on the first

floor. If you don't find the manual you are looking for, you can call for help in the

aivo mailing list.

Most Macs accept normal 3.5'' diskettes and some CD-ROMs and 100 MB ZIP

diskettes too. Portable ZIP drives are available.

PRINTERS

You can print your documents with any of the following printers, provided that your

computer is connected to the Ethernet, and that you have in your computer the correct

settings for the printer that you want to use.

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Glyph

Glyph (HP LaserJet 4000TN) is the default printer in all UNIXes, and those

Macintoshes that are on the first floor, like Glyph itself. It can print greyscale images.

Sans

Sans (HP LaserJet 4000TN) is the default printer in the Macintoshes on the third

floor, where it is located. Sans is a greyscale printer.

Papyrus

Papyrus (HP DeskJet 1600CM) is an inkjet colour printer located in the first floor

corridor. Papyrus is good for making colourful overhead transparencies.

Hiero

Hiero (Tektronix Phaser 840) is a wax printer for the best-quality colour printing on

normal laser transparencies, or normal copy paper. It is located in the computer room

(F157, the one with an iron door on the first floor).

SCANNER

A scanner is available in Dr. Peter Berglund's office (F147).

UNIX ENVIRONMENT

In HP-UNIX, you can start the e-mail program, File Manager, Application Manager,

Print Manager, or Style Manager by clicking the respective icons only once with a

mouse. After that, you have to double-click to open a folder or an application, just like

you would do when using Windows.

E-mail program

If you have new mail, the e-mail program icon changes slightly: the envelope pops

out of the mailbox. If the envelope is in a horizontal position, you don't have new

mail. In order to save disk space, please delete all e-mails you don't need in the future,

especially if they contain large attachment files.

Text Editor

Text Editor is opened by clicking the paper-and-pencil icon. The editor is very robust,

but includes e.g. the Find and Replace commands.

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Terminal Window

A submenu containing Terminal Window icon is opened by clicking a small

triangular arrow on top of the Text Editor icon. In the terminal window, you can give

UNIX commands. The most useful commands are listed in the following table.

man Type man command to get help using any command. E.g. , try: man ls.

pwd Print working directory. Tells the path of the directory you are in.

ls List of items in the current directory.

ll List of items in the current directory including size, date and permissions.

cd Change directory. Plain cd changes to your home directory, cd x changes to

directory x, and cd .. goes up one directory in the path.

cp Copy. Saves the original.

mv Move. Deletes the original. It is safer to use cp (and afterwards rm),

especially if moving large files through the net.

rm Remove. Deletes the file. Use this command instead of the trash can on the

desktop of your computer.

chmod Changes reading, writing and executing permissions of files and folders.

top Shows the processes which are running on your computer and how much

they spend your computer's resources. Press Ctrl-C to stop this process.

ps Lists ongoing processes.

kill To kill process number xxxxx, type kill xxxxx.

bdf Reports the number of free disk blocks.

File Manager

With the File Manager, you can e.g. move, rename and copy files, make new

directories, and change permissions without having to remember the appropriate

UNIX commands.

Application manager

Of several possibilities, you will need most likely only those applications that are in

the Neuromag folder. You will see the Neuromag applications by double-clicking the

Neuromag icon. Some of them are listed in the following table.

Data To mount or demount MOD drives, or to initialize MODs,

drop the correct volume icon (e.g.

"Volume:pleasureMOD") to either "MountVolume+",

"UnmountVolume–", or "InitVolume" icon, respectively.

DiskSpace Tells the amount of free disk space on all hard drives or

MOD drives that are available.

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Manuals Manuals for most Neuromag applications can be found

here.

Acquisition The data acquisition program, runs on Pleasure

workstation only.

Plotting A data plotting program. Good for quick and dirty on-line

analysis of data.

Graph-beta A powerful tool for signal analysis, mainly for

spontaneous data.

MCE-beta A data analysis program for calculation and visualization

of minimum norm estimates.

SourceModelling A data analysis program for dipole fitting.

MEG-MRI-integration A program for visualization of dipoles on MRI scans.

MRI-segmentation A program for manipulating MR-images.

ViewBrain A program for viewing the surface of the brain.

NeuroTerminal A terminal window which has some settings different from

the ordinary terminal window. To run Netscape, type

netscape in the NeuroTerminal. To run Acrobat Reader,

type acroread in the NeuroTerminal. If you want to use the

window for other purposes while Netscape is running,

write netscape&.

Style Manager

Here you can modify many settings that influence how the desktop looks like. Make

sure that you set the Screenlock off (under the Screen icon) to allow other persons to

log in when you are away.

Desktops

In the UNIX environment, you have a number of desktops available (the default is

four, but you can have more). You can modify them to suit your purposes.

MAGNETO-OPTICAL DISKS

Many of the UNIX workstations are equipped with a magneto-optical disk (MOD)

drive. The MOD has to be mounted before you can use it. To mount an MOD, go to

the Application Manager–Neuromag–Data folder and draw the icon bearing the name

of the MOD drive (e.g. pleasureMOD) onto the MountVolume+ icon. Before taking

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the MOD away from the drive, you have to unmount the disk in the same manner,

except that now you draw the correct volume icon onto the UnmountVolume– icon.

Before you can start to write files to an MOD, you have to initialize the disk by

dropping the correct volume icon onto the InitVolume icon. Both sides of the MOD

have to be initialized separately. Fortunately, you only have to do this when you are

using the MOD for the first time, whereas mounting has to be done every time when

you use the MOD. Mounting, unmounting and initializing takes some time, and you

probably have to answer yes to some questions that the program poses during the

processes. Please label the MOD clearly with your name, project, and date.

SAVING EVOKED RESPONSES AND RAW DATA

When saving evoked responses or raw data at the workstation Pleasure, please save

your data elsewhere than to the pleasuredata hard disk, despite that the Acquisition

program gives this option as a default. Instead, save your data to e.g. the newdata hard

disk, any of the temp hard disks, or to an MOD. These measures have to be taken

because (1) the disk space in pleasuredata is very limited; (2) the pleasure workstation

can crash if the pleasuredata hard disk is full; and (3) when reading data in the

pleasuredata hard disk from a remote workstation while someone else is using the

Acquisition program in the measurement room, the Pleasure workstation can crash.

When saving large raw data files, it is recommended that only MODs or temp hard

disks be used. For example, you can first save the data to a temp hard disk, and later

downsample them to an MOD. Downsampling means saving of the data in such a

form that only every second (or third, or ...) data point is saved. All data saved to a

temp hard disk will be lost automatically after one week.

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3. Working in the measurement room

The measurement room (room 159) contains a computer space, a space for preparing

the subject, and a magnetically shielded room (MSR), where the Vectorview device is

located.

More than thirty people use our Vectorview system in their experiments regularly.

Therefore, it is of crucial importance that everyone follows guidelines of laboratory

safety and good laboratory practice. The Vectorview system is completely safe when

operated correctly, but you have to know some potential hazards that may result from

carelessness or thoughtlessness. When leaving the measurement room, please check

that it is in as good condition as it was before you started working.

RESERVING A MEASUREMENT TIME

You have to book a measurement time before you can start MEG recordings. The

reservation lists are located in the measurement room, to the left of the entrance.

There are two sets of lists. The calendar of planned usage, which has names printed

on it, is on the left hand side. The actual usage list is on the right. Those people

whose names are mentioned in the planned usage list have a priority to use the room

at times that are allocated to them. You may not reserve somebody else's

measurement time without permission. The earlier you start to negotiate on getting a

certain time slot, the better your chances of getting it. You may have to give your own

time slot in return for the slot you want. To confirm that you are going to use a certain

measurement time, mark your name clearly on the actual usage list preferably two

days in advance. If you have to cancel your measurement time, please strike your

name out of the list as soon as possible.

Possible measurement times on weekdays are 8–12 a.m., 12 a.m.–15 p.m., 15–18

p.m., 18–21 p.m. and 21 p.m.–8 a.m. On weekends, the possible time slots are 8 a.m.–

14 p.m., 14–20 p.m. and 20 p.m.–8 a.m. However, measurements are rarely done in

the night, as it is difficult then to get subjects and keep them awake. Please don't

exceed your measurement time, because the next person has to be able to start on

time.

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The helium refill takes place on Mondays from 12 a.m. to 15 p.m. It is not possible to

measure at that time.

OPERATING VECTORVIEW

Vectorview's manual can be found in the measurement room. Please take a look at the

manual before you do anything. Your tutor will teach you how to record. The

Acquisition program manual, as well as most other manuals, can be read with the

Acrobat Reader program in UNIX systems. You'll find the manuals under Application

Manager–Neuromag–Manuals icon. You can print hard copies of manuals for yourself

if needed.

STIMULATION SYSTEMS

Kimmo Uutela has written a short manual about stimulation systems. You'll find the

manual in the measurement room. Typically, MacProbe program running in the

Stimulus Mac is used for controlling the flow of stimuli. Simple stimulus sequencies

can also be controlled by the Acquisition program.

There are two systems for auditory stimulation, the lo-fi system (Nicolet Tip–10) and

the hi-fi system (UD ADU 1a). The lo-fi system is the choice when using frequencies

below 4 kHz. The hi-fi system is good up to 12 kHz. If using the lo-fi system, see that

you don't throw the small plastic connectors between eartips and silicon tubes to

trashes. This has happened many times.

When using visual stimuli, remember to turn off the data projector (Electrohome

VistaPro) after use and place the hood over the periscope. Take care of the mirrors

and filters and don't touch them without special gloves.

For somatosensory stimulation, we have a two-channel electric stimulator and an

eight-channel tactile stimulator available. For more information about stimulation

systems, see the Stimulation systems manual.

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MAGNETICALLY SHIELDED ROOM

Protecting Vectorview from magnetic contamination

The Vectorview system comprises 306 thin-film superconducting interference devices

(SQUIDs). The sensors are ultrasensitive in the sense that they can pick up changes in

magnetic field in the range of femtoteslas. This is why the Vectorview system is

placed in a magnetically shielded room (MSR). Bringing magnetic objects close to the

Vectorview device can cause flux trap in the SQUIDs, which may lead to a long and

expensive service break and delay the measurements.

Before entering the MSR, please remove any potentially magnetic objects that you

may be carrying. These include belts, keys, watches, coins, hairpins, eyeglasses and

pieces of clothing with metallic parts. Also cameras, flashlights, mobile phones or any

other electrical equipment are strictly forbidden. Never take a bar magnet inside the

MSR. To prevent any magnetic dust from getting into the MSR, always take your

shoes off before going in. Tell your visitors and experimental subjects from outside

the BRU about these restrictions and see that they behave appropriately.

Don't leave any equipment in the MSR (exceptions: periscope and its hood, screen,

auditory and somatosensory stimulators, response pad, and emergency door handle).

You can place your experimental equipment in one of the cupboards outside the MSR.

To prevent microscopic magnetic particles from causing spurious results, don't attach

anything (e.g. tape) to the Vectorview helmet. Furthermore, don't touch Vectorview

unnecessarily and keep a respectful distance from the device.

If you don't know whether some object is magnetic or not, you can test it, but in the

presence of an experienced MEG researcher only. In the test, somebody waves the

study object inside the closed MSR and somebody else watches the raw data display.

Before you take the object in, make sure that it is not a bar magnet. Start two meters

away from the device and wave your bare hand to see that you are not magnetic

yourself. Then proceed towards the Vectorview little by little. If your colleague sees

artefacts on the raw data display, then the object is magnetic and you should avoid

bringing it inside the MSR.

Monitoring the subject

During measurements, you can communicate with the subject by means of a two-way

voice intercommunication system (Stentofon). Dial 8 to open the connection and C to

close it. Keep M pressed while talking to the subject. The microphone is very

20

sensitive, so you can keep an arm's distance to the Stentofon when talking. While the

Stentofon is on, you can hear all the time what the subject says, except when you are

pressing the M button. You can monitor the subject on the TV screen.

Forcing the door open

Note that you can use the yellow door handle, based on two suction cups, should the

MSR door not open by pressing the "open" button. In such an emergency, press the

red "emergency" button to release the pressure that keeps the MSR door closed. Then

attach the yellow door handle on the door and force the door open.

LABORATORY SAFETY

Safety comes always first, no matter how important the experiment is. In the

measurement room, same rules apply as in any laboratory. Some additional points,

special to the BRU, are worth stressing. You are not allowed to start measurements

before reading this section carefully.

Moving the Vectorview probe unit

The Vectorview gantry can be either in a lying position or in a sitting position.

Usually the gantry is in a sitting position, but for example during the helium transfer

on Mondays the gantry is in a lying position. The gantry can be lifted and lowered

easily by pushing two buttons that are behind the gantry (arrows up and down). When

the buttons are pushed, the gantry is lifted or lowered by ropes that are connected to a

motor outside the MSR. During measurements, the gantry rests on two claws, both of

which alone should carry at least four times the weight of the gantry. However, when

the gantry is hanging from the ropes only, the probe unit can fall down if something

unexpected happens, causing a serious mechanical injury to the subject. The weight of

the probe unit with liquid helium and the supporting frame is 270 kg.

The "traffic lights" behind the gantry indicate whether it is safe to place a subject

under the dewar or not. The green light indicates that the gantry is resting safely on

the claws. You may place a subject under the dewar only when the green light is lit.

The yellow lights indicate that there is tension in the ropes or that the gantry is in an

extreme position (where it should not be). The red light indicates that something is

wrong and you should contact the service personnel. If you notice that the green light

is not lit and the subject is already sitting under the dewar, first take the subject away

and only after that move the dewar. Never move the probe unit while the subject is

sitting under the dewar.

21

Dealing with liquid helium

Read the Vectorview manual section that concerns the properties of liquid helium.

The dangerous properties of helium are (1) its extreme coldness when liquid (–269

˚C); (2) its tendency to displace oxygen in the air; and (3) its tendency to expand in an

explosive manner when transforming from liquid to gas in room temperature. Be

aware of the dangers if watching the helium transfer in the measurement room or if

visiting the helium liquefier workshop (room F130).

The cryogenic dewar of Vectorview, containing maximally 70 litres of liquid helium,

has several mechanisms to ensure that the dewar should not leak. However, if you

hear any hissing sounds coming from Vectorview, it is time to get out of the MSR and

contact Veikko Jousmäki or Neuromag personnel.

Keep an eye on the subject

Never leave a subject or a patient unsupervised in the MSR! If someone is inside the

MSR, don't leave the measurement room even for a short while, unless someone else

replaces you. Someone must be available for help if the subject suddenly has an attack

of illness, or if something unexpected happens.

Fire, acute illness, or other serious emergency

The general emergency telephone number is 112, but when calling from HUT you

have to dial 0 112. You can call an ambulance, the fire brigade, and the police from

the one and the same number, 112. Be calm, answer the questions clearly, and don't

hang up before you're permitted to do so. A comprehensive first aid kit, for the use of

qualified personnel only, is located in the measurement room in a cupboard under the

washbasin. The first aid kit is in a big blue metal box. It contains some drugs for

resuscitation, and some against epileptic seizures.

SOURCES OF ARTEFACTS

Always check how the MEG channels look like before the subject enters the MSR. If

the channels appear noisy or "sleeping", there can be several reasons for that. First,

read the Vectorview logbook. Compare the present noise level with the figures

between the leaves of the logbook. You may find that the problem is known and

incurable.

The sensors can be "trapped" or in a bad tune. You can try to heat individual sensors

and reset channels with special commands in the Squiddler program. Usually this

22

helps. If you think that the device is in an especially bad tune, contact the person who

is in charge for tuning. Don't tune by yourself, or if you do (and know what you are

doing) report all changes in the logbook.

If the channels appear noisy only after the subject has entered the MSR, check that the

subject does not have anything magnetic on. Slow drifts may be caused by

respiration-related movements of necklaces, T-shirts with colourful figures, metallic

buttons, brassières... Does the subject's heart cause the artefact? Does the subject

contract muscles? Is the subject or somebody else moving in the MSR?

There are several possible external sources of noise. One common phenomenon is the

interference from the neighbouring cryogenic instruments. On the other side of the

wall, three research groups (INTERFACE, NANO and ROTA) study physical

phenomena in low temperatures. Sometimes they have to magnetize or demagnetize

their cryostats, which can cause so big artefacts that it prevents any MEG

measurements. The LTL physicists are supposed to inform about their magnetizations

and demagnetizations well in advance in the aivo mailing list. You can ask the

physicists kindly to postpone their procedure, especially if you have an important

experiment going on and if the warning has come in the last moment. Be diplomatic

— also they have important research to do, just like you.

When visiting the measurement room while someone is recording, don't slam doors

— this would cause an artefact to the MEG.

WHEN LEAVING THE MEASUREMENT ROOM

Before leaving the measurement room, please check that

- you have logged out from Pleasure workstation;

- you have put all the things back to the same place where you took them;

- you have removed all 2-sided tape from electrodes, HPI coils and Vectorview

gantry;

- you have cleaned the electrodes with a toothbrush so that there's no paste left;

- the electrode wires are not tangled;

- you have taken your belongings (keys, coffee mugs, papers...) with you;

- you have returned empty bottles where they belong;

- the room is as clean as it was before you came.

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If you are the last person to do experiments on that day, please check that

- the MSR lights are off;

- data projector is off;

- MSR door is closed;

- TV monitor and Stentofon are off;

- auditory and somatosensory stimulus systems are off;

- measurement room lights are off.

4. Afterword

This guide may have felt like an exhausting list of dos and don'ts. However, my aim

has not been to discourage you. It is natural that learning new manners of doing things

takes several months. Many things may have been left unsaid, but common sense will

take you far. To conclude, enjoy your stay and your science!