The spring's users' meetings

Here are the dates on which we plan to hold users' meetings during the spring (always at 11.00 in the R43 conference room):

8/2, 8/3, 5/4, 3/5 and 7/6.

Season's greetings

The manager wishes everyone a Merry Christmas and a Happy New Year!

Cancelled users' meeting

The users' meeting on the 11th of January has been cancelled, so that the next meeting will take place on 8th of February instead.

The next neuGRID meeting

The next neuGRID meeting will take place January 24-26 in Brussels. This will constitute the Final event, where the project is unveiled to scientific community. An agenda will be posted here later on. A training session for key researchers within the community will also be held during these days, with the help of some of the SMILE users. We are currently organizing internal practice events on using the grid to prepare ourselves for this.

2011 spring talks

Here is the schedule for the spring academic meetings -- quite a packed one!

Academic meetings at SMILE, spring 2011:

Thursday 13/1 at 11.00 in the R43 conference room:
Gabriela Spulber (PhD student at Institute of Clinical Medicine/Neurology at University of Eastern Finland, Kuopio and Department of Neurobiology, Care Sciences and Society, Division of Clinical geriatrics, Karolinska Institute):

”Visualizing normal aging”


Thursday 20/1 at 11.00 in the R43 conference room (extra meeting):
Amirhossein Manzouri (Exam work presentation for the Master’s degree in Medical Imaging at KTH):

“Tract based statistics of white matter analysis: clustering versus ROI”


Thursday 27/1 at 11.00 in the R43 conference room:
Olof Lindberg (PhD student at Department of Neurobiology, Care Sciences and Society, Division of Clinical geriatrics, Karolinska Institute):

“The frontal lobe: at conceptual, structural and functional levels”


Thursday 3/2 at 11.00 in the R43 conference room (extra meeting):
Stefania Geraci (Exam work presentation for the Master’s degree in Electronic systems for biomedical applications at Department of electronics, informatics and system science at University of Bologna, Italy):

“Reduction of pulse artefacts in EEG data recordings at 3T”


Thursday 10/2 at 11.00 in the R43 conference room (extra meeting):
Victor Alvarez Barrientos (Exam work presentation for the Master’s degree in Medical Imaging at KTH):

“Brain image processing for revealing early Alzheimer's disease signs”



Thursday 31/3 at 11.00 in the R43 conference room:
Anna Gärdin (MD, PhD student at Department of Clinical Science, Intervention and Technology at Karolinska Institutet, Division of Medical Imaging and Technology, and Department of Radiology):

"MRI in chronic Achilles tendinosis"


Thursday 21/4 at 11.00 in the R43 conference room:
Xiaozhen Li (PhD student at Department of Neurobiology, Care Sciences and Society, Division of Clinical geriatrics, Karolinska Institute):

"Assessment of AD risk with novel MRI techniques"


Thursday 26/5 at 11.00 in the R43 conference room:
Lena Cavallin (MD, PhD student at Department of Clinical Science, Intervention and Technology at Karolinska Institutet, Consultant in neuroradiology):

"Visual assessment of MTA is good enough... "

Coffee filters

We now have more coffee filters in the kitchen.

Book project "Neuroimaging"

Lena Cavallin was invited to participate in a book project, but had to decline the offer. It is however open for contributors (Open Access), so if you are interested, contact Sandra Bakic (see below).

Here is the detailed information:

My name is Mrs. Sandra Bakic and I am contacting you regarding a new InTech book project under the working title "Neuroimaging", ISBN: 978-953-307-413-9.

This book will be published by InTech - Open Access Publisher covering the fields of Science, Technology and Medicine.

You are invited to participate in this book project based on your paper "Voxel-based correlation between coregistered single-photon emission computed tomography and dynamic susceptibility contrast magnetic resonance imaging in subjects with suspected alzheimer disease", your publishing history and the quality of your research. However, we are not asking you to republish your work, but we would like you to prepare a new paper on one of the topics this book project covers.

Publication of the book is scheduled for 25 July, 2011. It will be abstracted and indexed in major online repositories and search engines. The book will also be available online and you will receive a hard copy via express delivery service.

Why should you participate?
- "Neuroimaging" covers your area of research
- Free online availability increases your paper's impact
- Each InTech book chapter is downloaded approximately 1000 times per month
- More citations of your work (research findings indicate that papers published under the Open Access model are likely to enjoy increased citation rates)
- You keep the copyright to your work

NEXT STEP: For further details about this book project please visit

http://www.intechweb.org/welcome/e4321a4d45346699f9ada729290e156a/lena.cavallin@karolinska.se

On this page you can find a detailed description of the book project, its scope and topics, details of the publishing process and a registration form.

For further details about InTech and Open Access please visit:
- About InTech: http://www.intechweb.org/welcome/e4321a4d45346699f9ada729290e156a/lena.cavallin@karolinska.se#about
- About Open Access: http://www.intechweb.org/welcome/e4321a4d45346699f9ada729290e156a/lena.cavallin@karolinska.se#oa

If you need more information about this book project, InTech or Open Access, please don't hesitate to contact me.

On behalf of InTech President, Aleksandar Lazinica,

Mrs. Sandra Bakic
Publishing Process Manager
---
InTech - Open Access Publisher
Email: bakic@intechweb.org
Web: http://www.intechweb.org/

Dr. Howner

Congratulations to Katarina Howner (previously Wahlund) who made a brilliant defense of her thesis today!

Going to Geneva

The manager will together with two users participate in the last neuGRID quarterly meeting, held in Geneva, Switzerland, on 6-8 of December. Hopefully we will see some more of the graphical user interface and have our example pipelines put through a fully functional grid!

TEDx event at KI

There will be a first TEDx talk at KI on the 15th of December (read more about TED here). The event is organized by the KI Development Council and will take place at Nobel Forum, Nobels väg 1, Karolinska Institutet Campus Solna. Reception will be opened at 12:30 and the event starts on the stage at 13:15. You can find the full program here.

Now running Ubuntu...

Freja and brage are now both running on Ubuntu. A positive effect of the switch is that printing again works from the Linux machines! Brage also has a functioning CD reader again (due to clever scavaging of old parts by Carlos and Victor).

We need to think about if brage should again be set up as a slave to freja or if we want it to be a free-standing machine. This will be discussed at the next user meeting.

Glögg party!

On Wednesday 15th of December at 15.00 it is finally time again for the yearly SMILE glögg party! We'll meet in the R43 conference room for some glögg and gingerbread and mingling. All are welcome to participate -- just tell me so at the latest on Monday the 13th.

User meeting moved

According to schedule, this year's last users' meeting will be held on 7th of December. However, many regular participants (including myself and Carlos) cannot attend that date, so we have decided to move the meeting one week ahead. Thus the last users' meeting of the year will be held on Thursday 14th of December at 11.00 in R43.

Ubuntu

We are moving the Linux computers (both freja and brage) to run on the Ubuntu operative system instead of as previously on Red Hat. Backups are of course made and all software will be reinstalled on the new systems, but during the switch your account will not be accessible. The switch is expected to be complete during next week.

Hermes OK again

As of yesterday, the Hermes system is again fully functional.

Study subjects wanted

Ivanka Savic-Berglund and Andreas Olsson are looking for study subjects for a research project on emotional stimuli. The subjects need to be Swedish-speaking, right-handed women 30-45 years of age who use estrogen-type contraceptives. A compensation of 800 SEK is given for participation. Please see the notice on the SMILE pinboard or contact the manager in case you are interested!

Hermes: az and obelix

Hermes personel have updated the az workstation. However, the obelix server is full so at present GOLD programs cannot be run. Leif is working to fix this problem.

New talk added

We have a new talk added to the academic meeting series, on Thursday 2nd of December (at 11.00 in the R43 conference room):

Katarina Wahlund (PhD student at Department of Clinical Neuroscience at Karolinska Institute, Stockholm): Offenders with mental disorder: psychosocial and neurobiological aspects

All are welcome!

New on freja

New and updated programs on freja:

LONI pipeline
MRIcro and MRIcroN
XMedCon
LCmodel
VBM
Java and Firefox

Cancelled talk

The talk this Thursday (27:th) by Gabriela Spulber has had to be cancelled due to illness. The talk will be given at another academic meeting instead.

Hermes az service

At some point this week Ronnie from Hermes will do service updating of the julius server and az client, during which time the system will be unavailable.

Forwarding of blog entries

I have just woken up to the fact that the blog entry summaries have not been sent out for several months. I think I have identified the problem now, so consider this post a test...

Clean up Hermes desktops, please!

The Hermes Windows machines have many, many files lying on the desktop. Please backup and remove as files will be deleted shortly!

Also, several programs have been downloaded without prior permission (as the data contract clearly states must not be done). The settings of the hermes user has been changed so that this is no longer possible.

New conference website

There is a new website which gathers information on conferences worldwide, hosted by EDP Sciences. Take a look at

http://www.webofconferences.org/index.php?lang=en

Matlab learning event

As previously noted on the emailing list, there will be a Matlab learning event at SMILE, given by Carlos.

The first meeting will be on Monday 18th of October at 15.00 in the R43 conference room. Carlos will give an initial talk introducing Matlab for those of you who are interested in learning the language: no previous knowledge of Matlab or programming is needed. In this first meeting the plan is to cover the basis (from zero), so even those who have never seen or used Matlab can feel comfortable.

New posters now on display

We have had a large influx of posters to Imagelab, mostly from this year's ICAD conference. The walls are now bursting with them -- you are welcome to come over and have a look! Remember, we will always be happy to have posters donated to the lab...

Invitation to Mehregan

Our exam project student Amir is cordially inviting everyone to celebrate Mehregan at KTH tomorrow! The party is organised by PerSiS (Persian students in Stockholm) and this is their description of the event:

It is time to celebrate MEHREGAN the second most important traditional Iranian festival to honor “MEHR”, which means friendship, affection and love. It is also widely referred to as Persian Festival of Autumn. This festival starts with a cultural event and follows by a BIG PARTY which makes it an unforgettable night. Special part: Mehregan Traditional Table (don’t miss it) Bring cash with you! Drinks (Alcoholic and None) and snacks are available to buy. Entrance fee for students 50 SEK, non-students 100 SEK.

Time:
Tomorrow Friday 8th of October at 7:30pm - Saturday at 1:00am

Location:
KTH, Main campus, Nymble(Main entrance)

User practice -- LONI

Today we will hold the first practice event preparing ourselves for the final testing round of neuGRID in Geneva in December. During the autumn we are planning several such occasions, studying

• the LONI Pipeline Processing Environment
• the gLite middleware for communicating with the grid
• neuGRID computing itself

Today Carlos will hold an introduction to LONI, a tool with which it is possible to graphically put together workflows for processing images (no scripting needed!). We will meet at at 15.00 in the R43 conference room.

All are welcome!

A seminar in shape theory

I had a tip from Ozan Öktem about an upcoming seminar which deals with recent developments for mathematical methods applicable to shape recognition and classification.

Here is the detailed description:

Time: Wed 2010-09-29 kl 13.15 - 15.00
Place: Room 3733 Lindstedtsvägen 25
Contact: Ozan Öktem (790 6606) or Sandra Di Rocco (790 7168)
Weblink: http://www.kth.se/sci/institutioner/math/kalender/2.21854/seminars/an-overview-of-computational-anatomy-1.65738

An overview of Computational Anatomy
Joint CIAM/Algebra and Geometry Seminar by Stéphanie Allassonnière from Centre de Mathematiques Appliquees, Ecole Polytechnique.

The seminar will provide an overview of Computational Anatomy which is an emerging discipline at the interface of geometry, statistics and image analysis, that aims to analyse and model biological shape variability at the population scale. The goal is not only to model the normal mean anatomy and its normal variations among a population, but also to discover morphological differences between normal and pathological populations, and possibly to detect, model and classify pathologies from structural abnormalities. Another goal is to correlate this variability information with other functional, genetic or structural information.

First, the goals and mathematical tools which are needed for such methods are presented. In particular, the focus will be on the deformable template framework, which assumes that the shapes that come from a given group (in term of age, sex, disease) are close to each other up to a class of deformations.

Next, the registration issue is introduced which is the central tool in this context. Its goal is to find the 'optimal' deformation that maps one shape onto another one. Some techniques which have been proposed to solve it will be presented bringing us to the Large Deformation Diffeomorphic Metric Mapping (LDDMM). This mathematically well-grounded method allows one to consider the registration of landmarks, curves, surfaces and images within the same framework.

The last part of the presentation will focus on the probabilistic and statistical questions that arise when we are provided with a population of images or shapes. The main issue is how to compute a "mean" and a "deviation" from this set. The main tools and results will be introduced whereas a more specific tutorial given the day after will discuss further issues.

Stéphanie Allassonnière received her PhD in 2007 from the Université of Paris 13 (France) in Applied Mathematics . The thesis was supervised by Alain Trouvé (ENS- Cachan) and Laurent Younes (CIS - Johns Hopkins University, Baltimore) and dealt with statistical estimation of template images using generative models. She then spent one year as a postdoctoral fellow in the CIS working with Laurent Younes and Michael Miller on statistics for medical imaging. Since 2008, she have been Assistant Professor in Ecole Polytechnique in the Applied Mathematics Department where she has continued her research on statistical analysis of images and deformations. In particular, she is studying the mathematical properties of the statistical estimators and stochastic estimation algorithms. She was recently awarded the "Prix Excellencia 2010" for her research work.

New seminar on the seminar list

I've added one more seminar to the academic meeting series list. Make room also for

Thursday 11th of November:
Love Nordin (PhD student at Department of Clinical Sciences, Danderyd Hospital): Detection of drug related cortical responses and pathophysiological mechanisms by using arterial spin labelling MRI techniques

ARC lecture

Anna Rieckmann invites you all to the lecture on Thursday, the 30th September, 10.00 - 12.00 by Dr. Marco Catani entitled "Defining the anatomical complexity of human networks" at the Aging Research Center (Gävlegatan 16). She thinks that this lecture may be of interest to many SMILE members!

neuGRID user test meeting, Brescia

Four of the lab's users (+ our previous guest Julia Miralbell) helped out with the second round of grid testing in Brescia during September 6-8. More functionalities had been implemented, and our users contributed with valuable feedback on the look and feel of the neuGRID user interface.

User meetings

The remaining user meetings during the autumn will take place on:

Tuesday 12/10
Tuesday 16/11
Tuesday 7/12

Autumn academic seminars

Here is the list of the seminars planned (so far!) in the autumn's academic meeting series.

Thursday 7th of October:
Eric Westman (PhD at Department of Neurobiology, Care Sciences and Society, Division of Clinical geriatrics, Karolinska Institute): A report from ICAD 2010

Thursday 14th of October:
Daniel Ferreira Padilla (PhD student at Psychobiology and Methodology Department, Faculty of Psychology, University of La Laguna, Tenerife, Spain): Image analysis under FreeSurfer: NGF dataset as test images

Thursday 28th of October:
Gabriela Spulber (PhD student at Institute of Clinical Medicine/neurology at University of Eastern Finland, Kuopio and Department of Neurobiology, Care Sciences and Society, Division of Clinical geriatrics, Karolinska Institute): TBD

Thursday 18th of November:
Tracing students (Linnea Engström, CH Ehrenkrona, Nathalie Thomé, Jenny Åström, all undergraduate students at Karolinska Institute): Manual tracing of the hippocampus, the anterior cingulate cortex and the entorhinal cortex

Thursday 25th of November:
Michael Schöll (PhD student at Department of Neurobiology, Care Sciences and Society, Division of Alzheimer Neurobiology, Karolinska Institute): Application of PET in Alzheimer's disease

Thursday 16th of December:
Martin Uppman (PhD student at Department of Clinical Science, Intervention and technology at Karolinska Institute, Stockholm): Integrating EEG and MRI

Starter Kit

I have produced a SMILE Starter Kit for all new users and anyone who feel they would like to brush up on how the lab works. It details among other things the various computer systems and softwares we have available here, our meeting series, the data policy, how to gain access to the emailing list and much more. Please ask the manager for your own personal copy!

Call for exam work projects

If you have a suitable project for a master student's thesis work, please contact me as there have been requests for exam works coming in (and no doubt more will come in the coming months). I will add your project to the SMILE web page listing exam work projects -- http://www.smile.ki.se/education/exam_en.html -- and also put you in contact with students asking for projects.

Posters

If you have produced expensive posters with no other place to put them after the event than rolled-up in a corner -- remember that you are always welcome to bring them to SMILE, where we will be happy to display them on our walls!

Visitors and a new co-worker

We have at the moment two visitors at the lab:

• Daniel Ferreira Padilla, PhD student at Psychobiology and Methodology Department, Faculty of Psychology, University of La Laguna, Tenerife, Spain, from August 2nd to November 1st. He is working together with Gabriela Spulber in Lars-Olof Wahlund's group.
• Stefania Geraci from Department of electronics, informatics and system science at University of Bologna, Italy, from August to January 2011. She is performing her master's thesis work (Reduction of pulse artefact in EEG data recordings at 3T) with Tie Qiang Li as supervisor.

We also welcome Carlos Aguilar Palomeque who will be working part-time in the lab for six months, mainly helping out with the computers.

Long hiatus

There has been a long break in the blog entries, due to large workload. Hopefully I will have time to update a little more often during the autumn! To compensate, I will now make several entries at once about recent and upcoming events.

neuGRID users' mailing list

Though neuGRID is still not fully operational, you may be interested in joining an emailing list for neuGRID users. In that case, please contact the manager!

More news about the power cut

I have found out that the power cut will affect the card reader, so that it will not be possible to enter SMILE (the door will not work) during 07-12 on Monday 23rd of August. At the latest after lunch everything should be back to normal again!

Autumn Statistica courses

The Statistica catalogue sent to me gives a list of the Statistica Stockholm course dates for autumn:

STATISTICA BLOCK 1: 12-13 October, KS, Huddinge

and 9-10 November, KS, Solna

STATISTICA BLOCK 2: 11-12 November, KS, Solna

STATISTICA BLOCK 3: 1-2 December, KS, Solna

Interested? Read more about the Statistica courses at http://statsoft.se/utbildningar (only in Swedish: contact me if you need translation).

Prolonged power cut at R43

Due to the ongoing rebuilding of the power stations at the hospital, the power will be turned off at the R43 corridor on Monday 23rd of August from 07.00 to 12.00, when a new power station is installed for our location. All sockets with white labels will be powerless, but greenmarked sockets will still have power. The sockets at SMILE are all green (except for the ones by the white bench out in the corridor), but the internet connection will perhaps not work and there may be other hiccups during the day.

Matlab courses

The Mathworks offer courses in fundamental use of the software, programming techniques and more. See above for a list of courses, dates and prices (click on the image for a larger view). The manager can help you sign up for a course if you are interested!

Julia is leaving!

Julia is leaving us for Barcelona, but before she goes there will be:

a) Fika at 15.00 tomorrow Thursday in the lab

b) A "knytkalas" in Haga Park on Sunday! For details of the latter, check your mailbox for the latest SMILE mailing list message.

More coffee

There is now more coffee and tea in the kitchen. Hopefully it'll last a long time since I got two boxes of coffee instead of one -- seems as if coffee consumption increases in the summer time...

See the neuGRID video

The neuGRID project has produced a short (11.5 min) film describing the project, which you can see here. It is quite informative, and the manager plays a part in the movie! (For a larger screen, go to the video on vimeo via the link below).

neuGRID project from neuGRID Consortium on Vimeo.

After work!

There will be an after work event at SMILE on Wednesday 30th of June. We plan on going to O'Learys at T-Centralen around 18. Please sign up for the event on the whiteboard in the lab, as we plan on booking a table! (Or take your chances and turn up anyway...) Everyone is welcome!

The manager's vacation

I will be on vacation week 26, 29-31 and 34. Have a nice holiday, everyone!

Matlab, SPM5, SPM8 installed

Matlab has been installed on freja. Start it by simply typing matlab in a shell.

SPM has also been installed on freja, both version 5 and version 8. Start matlab, then type spm5 or spm8 depending on which version you want to run.

New guest arriving after the vacations

On August 2nd, our new guest will arrive for a three-month stay: Daniel Ferreira Padilla, PhD student at Psychobiology and Methodology Department, Faculty of Psychology, University of La Laguna, Tenerife, Spain. He will work together with Lars-Olof Wahlund's team.

Booking of freja

As the pressure on freja has increased as well, I have set up a booking list for freja similiar to the ones we already have in place for the Hermes machines. You can find it under Resources > Booking schedules on our webpages.

Upgrading of the card+code entrance system

The hospital is implementing a new card reader system for entering locked premises. To gain access through a door which has been fitted with the new system you will not have to swipe your card and enter a code but just hold your card to the reader, which will then open the door for you.

The implementation has already started, but thankfully at the other end of the hospital, so we will probably not be affected until autumn. However, I need to collect information about your cards already now in order to make the transition as smooth as possible. Please tell me at the latest on the 15th of July if you have:


a) a SIS-marked card. You'll find the SIS-mark to the left on your card.

b) an OSIS-card (similar to the SIS card but without the SIS-mark). Students at KI will at some point be given this type of card by their institution, I've been told.


I will send in lists with the holders of SIS/OSIS-cards to central management, who will then enter your card into the system.

All others have to use a K-badge for access (you don't need to check back with me if that is what you have). Unfortunately, the old K-badges will not work with the new system, so you will have to have a new badge made for you. The machine to produce such badges is not installed yet, so we will have to wait until autumn to get you set up within the new access system.

ICAD 2010

Several researchers associated with Imagelab will be attending ICAD 2010 (Alzheimer's Association International Conference on Alzheimer's Disease) in Honolulu on July 10-15, and are now preparing posters and talks. The researchers who will go there are Gabriela Spulber, Olof Lindberg, Eric Westman and Lars-Olof Wahlund. They will also attend an Innomed meeting while in the States.

On their return, their posters will be displayed in Imagelab -- which also means that some old ones will have to be taken down. I will not throw away the old posters but will keep them for future (exhibition) use, but if you have a darling poster which you want to keep on the wall, tell me so that I can consider how to structure the new poster display.

A great article about neuGRID

A really good article about the neuGRID project is now available online at the webapge of Future Medicine:

Grid infrastructures for computational neuroscience: the neuGRID example

Don't miss the visit by Metin Gurcan!

On Monday June 21 at 13.30-15.30 SMILE will be visited by Ass. Prof. Metin Gurcan from the Department of Biomedical Informatics at Ohio State University. Prof. Gurcan will be happy to discuss the projects of his lab (read more at http://bmi.osu.edu/cialab/) and will give an extra seminar at 14.30.

Don't miss this opportunity to hear about their state-of-the-art image processing software!

Clean your Hermes working folders!

Starting August 1st, all WORKING folders in the Hermes system will be set to purge data older than one day. This means you will have to save data that you want to keep from your working folders before this date, and that you will have to learn to always save data from working to archive folders.

On obelix the purge will be hard: data will be deleted. On julius the purge will be soft: data will be moved to your archive instead.

Hermes updated

This Monday the Hermes machines were updated by NUD. The Gold3 interface is somewhat different (but should be easily recognizable still), and there is now the possibility to couple other types of files (e.g. text, .doc, .pdf) to a patient. GOLD2 is also slightly updated.

It is now also much easier to import and export files in different formats from the Gold3 environment. You can choose beetween DICOM and IF and where to put your data (on a USB stick, for instance). N.B: it's only possible in Gold3, and you probably have to tweak your personal settings to make it work. There will be instructions in the red binder in the lab bookshelf about this shortly.

Fan to MAX

As stated earlier, the fan which cools the lab has to be turned on basically all the time. If you do turn it off, remember to TURN IT TO MAX when leaving the lab! That's right, crank it up to max! Otherwise the computers will be cooked in the summer heat... (no, it's not particularly warm outside, but it is easy to reach temperatures of 27 degrees in the lab).

End of the neuGRID meeting + testing results

After three hectic days, the neuGRID meeting has now come to a close. Several important issues were discussed (among other things the anonymization service), and the first user tests were held. These were a moderate success -- unfortunately the grid decided not to cooperate in full -- but several important lessons were learned, both for the developers and the participating test users from SMILE.

The next neuGRID meeting will be held on 6th to 9th of September in Brescia, Italy. We are currently discussing the possibility of bringing a few SMILE users down to Brescia to complement their pool of test users. The day earmarked for the tests will be the 7th of September. Contact the manager for more information!

The neuGRID meeting is in full swing

The June quarterly neuGRID meeting, hosted by SMILE, has now started. It takes place at KI during 7-9 June. Some 20 experts from all partners have gathered here to among other things perform the first user tests of the grid. Several SMILE users will help them, acting as evaluators of the grid functionalities that to date have been implemented. It will be really exciting to see how the tests turn out!

A web page about neuGRID

I have finally managed to put together a web page about the neuGRID project, which will hopefully clarify for you all what the project really is about...

You can find the web page here:

http://www.smile.ki.se/research/ng.html

Juha passed

Congratulations to long-time SMILE user Dr Juha Martola on successfully defending his thesis last Friday!

Experienced radiologist wanted

Virginija Karrenbauer and her collaborators are looking for an experienced neuroradiologist to participate in their new project which will investigate whether MS patients with and without oligoclonal bands in liquor have the same lesion patterns, and if there is a correlation with the HLA genotype. Shared first authorship is offered!

Her project description can be found at the SMILE webpages at

http://www.smile.ki.se/news/vk_en.html

or contact her directly at her KI address.

FSL vs SPM vs Civet

We had a really interesting presentation today by Julia Miralbell, who has been working together with Gabriela Spulber on the discrepancy between segmentation results performed with different softwares. A lively discussion took place about the various methods used by the softwares and possible error sources, and new tests were devised. We were also treated to lunch by Julia and Gabi!

Miika is back for a week

Miika Vuorinen, who visited us earlier during the spring, is back for a one week visit. So you may run into him in the lab this week!

brage

I have now fixed the "slave" machine brage in the sense that it is now possible to log on with your usual user name and password to access the data which was stored in the /brage folder. It is quite probable that many other things still do not function properly, but we will have to find those out as we go along. So, please report problems with brage to me!

neuGRID training and hands-on session

As I have previously mentioned, Imagelab will host the next neuGRID quarterly meeting, during June 7th-9th. As part of the work to develop neuGRID, a user testing session will be held, most probably on June 8th. During this session real-life users will sit down and try to execute two test scenarios on the grid, revolving around uploading data and performing an analysis pipeline on the data. Before that there will also be training, centering on how to create a certificate for the neuGRID website and how to log on to the portal.

In case you are interested in taking part in the neuGRID training and testing session, please contact me! We have room for 5-6 users, and 4 seats are already taken. Note that you as thanks for your services will be invited to the neuGRID social activity in the evening of the 8th -- a dinner cruise with m/s Stockholm to Vaxholm...

Julia stays a little longer

Our guest Julia Miralbell (PhD student at Department of Psychiatry and psychobiology, University of Barcelona, Spain) who is working in collaboration with Lars-Olof Wahlund,
will prolong her stay at SMILE by another month and a half. She will now return to Spain in mid-July. We're happy to have Julia with us for a while longer!

Dissertation by Juha Martola

Juha Martola will defend his thesis on Friday 28th of May, at 11.00 in the C1-87 lecture room. The title is "Brain volume reduction over four decades in multiple sclerosis" and you can read the thesis abstract at http://diss.kib.ki.se/2010/978-91-7409-815-0/


All are welcome!

Peter Aspelin on television

Peter Aspelin will be featured on Kunskapskanalen and give a lecture entitled "En tredimensionell resa genom kroppen", as part of the Karolinska Institute 200-year jubilee.

The show is in Swedish and will be aired twice:

Thursday May 27th 16.20-17.25
Saturday May 29th 12.35-13.35

Working on obelix is full

The working directory on obelix is much too full. It needs to be emptied in time for summer, when many students will produce a lot of ROI:s... If you have unsaved data in the obelix working directory, please take care of it before the end of next week! (Contact me if this is not possible for some reason). We will then remove all files from obelix working.

The fan

Sometimes people turn off the fan inside the lab (I do understand you, the noise results in poor working conditions). You really shouldn't though, since the computers will last longer if properly cooled.

However, if you do turn off the fan, turn the fan back on when leaving the lab! This will be especially important when summer approaches...

Data contract

As you may have seen or heard at the users' meetings, we will now start to implement the Data contract at SMILE. It is a simple contract which the board would like all SMILE users to sign, regulating (obivous) data protection issues such as never downloading illegal material to the SMILE computers or giving out one's password, as well as clearly stating that data will not be kept at SMILE indefinitely and that each user ultimately is responsible for data backup, among other things.

Please come by SMILE at your leisure to sign such a contract.

Extra academic meeting

One of the exam workers has been very quick in finishing his project and will give a presentation of his master thesis in Medical imaging at an extra academic meeting.

Thursday 3rd of June at 11.00 in the R43 conference room:
Carlos Aguilar Palomeque -- "Machine learning algorithm for studies in Alzheimer’s disease"

All are welcome!

neuGRID Best Demo

At the EGEE Forum in Uppsala, a competition was held among the participating posters/demos. The first prize went to neuGRID who by far outclassed all other participants!


Picture proof enclosed, from the aula at Uppsala University.

A reminder about bibliometry

Don't forget to verify your publications in the KI webcatalogue -- it is now also possible to do it for those of you with affiliations at SLL. In the future, funding will be distributed more according to the bibliometry. This is why it is so important that you always acknowledge SMILE in your papers...! See instructions here: http://www.smile.ki.se/publ/credit_en.html

You can go to a half-hour seminar on how to verify your publications, either on 11th of May or on 20th of May, both days at 14.30-15.00 in Birkeaulan.

Hermes -> valhall

The red SMILE binder in the lab has been updated with instructions on how to transfer data between the Hermes and the valhall system.

Exam work projects

During the spring we will have three exam workers doing projects in connection with SMILE. You can read more about what they will be doing at the new Exam work project page on the SMILE website! Here is the link: http://www.smile.ki.se/education/exam_en.html. In particular, Victor Alvarez Barrientos will also be helping out with the GSK medical study project.

Valborg lunch cancelled

Due to a combination of unfortunate events, the Valborg lunch outing to Uppsala has had to be cancelled. Hopefully we will manage to organize another event at a later point!

Jeffrey Looi in the lab

Today Professor Jeffrey Looi arrived at SMILE for a working visit of a week and a half. Welcome Jeffrey!

Looi talk moved forward

Due to a change in schedule, Prof. Looi has had to move his talk "Shape analysis of the neostriatum in frontotemporal lobar degeneration, Alzheimer's disease and controls" forward one day.

The talk will now take place on Wednesday the 28th at 11.00 in the R43 conference room. All are welcome!

Course in Imagelab on 4th of May

On the 4th of May, Gabi and Eric will be conducting an MR-imaging exercise as part of the course "Application of molecular biology and molecular brain imaging techniques in neurodegenerative disorders". This course is part of the postgraduate course programme The Neurosciences given by the Department of Neurobiology, Care Sciences and Society. The exercise will take part between 10-12 that day, so expect the Imagelab to be quite full then!

Valborg lunch, Uppsala

All SMILE users are invited to a Valborg traditional herring lunch in Uppsala! You will have to pay for the transport to Uppsala yourself, but the lunch is courtsey Lars-Olof Wahlund. Please tell me at the latest on Wednesday 21st of April if you wish to come! I will then send more details on how to get there etc...

Old freja files accessible

It is now possible to restore the backup file of old freja, meaning that stuff from the old machine can now be downloaded to new freja. Please tell me what files you wish to save, if any, as I will not unnecessarily clutter up the new disk with stuff that noone wants!

neuGRID second year review successful

Last week, the neuGRID project's progress after its second year of existence was evaluated in Brussels in the presence of reviewers selected by the EU commission. At this review I presented a user's bird's-eye view of neuGRID from the outside, which was very well received by the reviewers. Thanks to the efforts of the whole neuGRID team, the project passed the needle's eye and will receive funds for the third (and final) year. Yay!

Finally, more coffee

The coffee has been replenished in the kitchen.

neuGRID summer meeting moved

The neuGRID June quarterly meeting has been moved and will now take place at KI during June 7-9. We expect to organize a hands-on session with the purpose of 1) making users more familiar with the neuGRID environment 2) provide valuable feedback to the application constructors. All will be welcome to this event! More information about it later on.

Installations

The latest versions of FreeSurfer and FSL have been installed on freja.

Moving the users' meetings

Due to my upcoming absences, we will have to move the next two users' meetings.

The March meeting is moved from the 16th to the 23rd.

The April meeting is moved from the 20th to the 27th.

Both meetings will be held at 11.00 in the R43 conference rooms.

Eva's spring absences

During the spring I will take part in several meetings, conferences and courses. This means I will be absent from the lab the following dates (possibly with a day for travelling attached to the ends of the period):

15th - 19th of March: neuGRID meeting in Amsterdam
25th -26th of March: neuGRID second year review in Brussels
12th - 15th of April: 5th EGEE User forum in Uppsala
20th - 22nd of April: DCMTK (dicom toolkit) course in Oldenburg

In June (31st of May - 3rd of June) the neuGRID quarterly meeting will be held here at Karolinska, so you can expect me to be very much out of the office then too.

The latest from the lab

Many things have happened since I last had the time to update the blog...

* Congratulations to Yi Zhang on defending his thesis successfully!

* Old freja died, new freja is up and running but not yet up to par (e.g. the dicom server is not working)

* We have visitors, right now and upcoming:

-- Julia Miralbell (PhD student at Department of Psychiatry and psychobiology, University of Barcelona, Spain) who will stay until the end of May

-- Ariadna Besga (Postdoc at Carlos III Health Institute, Madrid, Spain) who will stay until the end of March but will be back later in the spring

--Jeffrey Looi (Associate Professor of Psychiatry at Australian National University Medical School, Canberra, Australia) will be visiting during 26th of April to 7th of May

* We have two exam work projects in the lab:

-- Carlos Aguilar Palomeque on "Machine learning classification of Alzheimer patients based on MR data" (currently running)

-- Victor Alvarez Barrientos on "Brain image processing for revealing early Alzheimer's disease signs" (starts in May)

* Oh, and Pierre left the lab on 16th of December for work elsewhere.