Final entry by old manager

So, I am leaving the lab, for new employment starting Dec 17th. I'd like to thank you all for the (almost) five years I have had the pleasure to manage the lab -- there have been some interesting challenges, a lot of good research done and most of all, so many nice people to work and have fun with. I have greatly enjoyed my time here and will miss you all!

 As of 1st of January, you will have not one, but two new managers. Karl Bodell will take care of the administrative duties (you will be able to find him in my old office at 25%), and Farshad Falahati will manage the computers (also at 25%). Kalle and Farshad, I wish you both best of luck at SMILE!

New version of PACS software

We have a new software called IDS7 for accessing PACS on the PACS-machine at SMILE. It is an updated and better version of IDS5, where you for instance can choose to download a single sequence only for a patient (remember, in IDS5 one was forced to download all sequences). IDS7 is started either by double-clicking the icon named "PACS Huddinge" on the desktop or by entering the address "http://pacshuddinge/ids7" in a web browser. Log on as usual with your HSA-ID and password. You can still also open IDS5 by choosing Sectra on the Start menu.

New postdoc in the lab

We welcome Daniel Ferreira Padilla who is starting a one year postdoc at NVS, Novum, on 1st of January.

Dissertation by Raffaella Crinelli

We congratulate Raffaella Crinelli on successfully defending her thesis on the 27th of November. The title is "When I show the Beatles then you say: "Ramones!" : imaging semantic memory in Alzheimer's disease and semantic dementia" and you can read the thesis at http://hdl.handle.net/10616/41226.

The big picture

Two months have passed since the last blog post and many things have happened. However, I have not updated the blog due to heavy workload, due to all the things to get ready before I leave for my new position. But here is a run-down of the most important things:

• SMILE did not get core facility support for the period 2013-2015 and is thus not formally a core facility as of 1st of January 2013. However, the board has decided that the lab will continue as before, with all functionalities intact. The board is at work mapping out the future directions SMILE will develop in, with data simulation being a core feature. 
• As a result of the above, the manager position will be diminished and also split in two: an administrative part and a computer part. The new administrative manager will be Karl Bodell. The computer manager position is as yet unfilled.
• Three new theses connected to SMILE have passed the test, and we congratulate Dr Julia Miralbell, Dr. Virginija Karrenbauer and Dr. Daniel Ferreira Padilla.
• We also congratulate Tie-Qiang Li and Rimma Axelsson on becoming professors at KI.

I will now leave for vacation (26th of October to 7th of December) and will work one last week at SMILE (10th-14th of December) before beginning in my new position.

Extra seminar on Aug 29th, 11.00

Even though the seminar list has not yet been quite finalized, we will have a talk tomorrow to "open the season". This extra seminar is given by Louise Blomkvist, and is a presentation of her recently finished exam work project at Medical physics, Stockholm university.

Title: Optimization of activity administration in myocardial perfusion SPECT

Place and time: Tomorrow Wednesday 29th of August, at 11.00 in the R43 conference room.
All are welcome to participate!

The manager is leaving in December

I have been offered and have accepted a new position as program coordinator at a company named Equalis, which means that I will be leaving Imagelab in just a few months. My official last day of work is Dec 14th, but I have a large amount of saved-up vacation which I graciously have been granted leave to use, which means that I will be gone during the period Oct 26th to Dec 7th.

Even though I am looking forward to new horizons I do regret leaving Imagelab, which has been an exciting workplace with interesting challenges and many friendly and talented people -- I will miss you all, but sometimes in life one needs to move on. I shall do my best to leave behind a tidy lab with no loose ends, in order to make the transition to a new manager as smooth as possible for you all.

Vacation

The manager will be on vacation counting from tomorrow. Back again on July 30th.

Coffee and tea

More coffee and tea has been added to the kitchen, to last over the summer. The tea comes in the form of a sampler with a large variety of flavours. Enjoy!

Dissertation by Julia Miralbell

Julia Miralbell will defend her thesis on Friday 13th of July, at 12.00 noon at the University of Barcelona in  Spain. The title is "Biomarkers of cognitive impairment and dementia". If you wish to read the thesis, please contact the manager who will supply you with a PDF. After the defense the thesis will be listed in the University of Barcelona's publication database, and a link to the thesis will be added to the SMILE webpages.  

Freesurfer in DN

Reading the paper on the train, I stumbled on a short notice (p 31 in DN on June 21st) about how the analysis of brain scans with Freesurfer differ significantly if they have been run on a Mac or a PC. Digging around on the net brought me to this article on PLoS ONE:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038234

Summer slow-down

Summer is here, and as a consequence there is less activity in the lab. The seminar series as well as the users' meetings will be on hold until August/September.

We plan for several courses during the autumn, but it is not too late to wish for learning activities. All suggestions are welcome!

Service of freja

Please note that service of freja has been reset to happen every second week instead of once a month. So, every Monday in an odd-numbered week freja wil be restarted.

IP-numbers, continued

Now the printer in the lab has a new IP-number and all machines have been reset to print to that number, so you do not need to worry about printing, it should work as normal. If you have a laptop that needs to be reconfigured, the manager can help you (or do it yourself -- the new number is written on the printer).

Also, az can connect to the web again. However, a restart of the machine could possibly mess that up, in which case the manager can fix the problem (but you should not restart the machine without the managers' permission anyway...)

Now all which needs to be fixed are the connections to the cameras, Sabb etc.

IP-numbers reset

So, the IP-numbers have now been reset in the lab. As stated earlier, please contact the manager if you need them.

As a consequence of the resetting, az can now no longer reach the net. We will try to solve this, alternatively ask Hermes support to help.

The printer IP has not changed however (another department within IT has to do this). We will be advised when this happens, but please tell the manager if the printer should suddenly behave oddly.

Workshop on statistical analysis of neuroimaging data

Information about the next workshop by Rita Almeida:

The next workshop on statistical analysis of neuroimaging data will be held on Wednesday, 30th of May from 9.00 to 12.30.

The first 2 hours will be held at the Tellus room, Dept. of Neuroscience, Retzius Väg 8, KI Solna.
The last part, the tutorial, will take place in the computer room Space, close to the library at the Solna Campus.

I will talk about methods used to study  connectivity using functional brain imaging data, with focus on fMRI. The workshop is organized as follows:

9.00-9.45 and 10.00-10.45: "Analysis of connectivity using functional brain imaging data" - in these two seminars I will review methods to study functional and effective connectivity from functional brain imaging data, with focus on fMRI.

11.00 - 12.30: Tutorial.

Please do register by sending the manager an email if you are planning to attend the workshop. In particular, it is helpful to know if you are following the tutorial.

Brain 101 cancelled

The lecture tomorrow by Lars-Olof Wahlund has had to be cancelled on short notice. We will however return in the early autumn (September?) with a broader program on the same theme.

No Linux course tomorrow

Due to the low number of participants, the Linux mini-course tomorrow (May 22nd) has been canceled. The next opportunity for learning more about Linux will take place in the autumn.

The 15-net is being closed down

On Monday 28th of May all IP numbers at SMILE will be changed, due to a policy decision by the hospital about the use and function of each number net. We will be given the new numbers shortly.

Please contact the manager ASAP if the IP number change will conflict with any activities you are planning to perform on the computers. Please also contact me if you need the new IP numbers for connecting remotely after next Monday.

Carlos and I will during next week work on re-setting SMILE's external connections to the MR cameras etc.

  

Dissertation by Olof Lindberg

Olof Lindberg will defend his thesis on Tuesday 19th of June, at 11.30 in the lecture room Hörsalen on floor 4, Novum, Karolinska Institutet, Huddinge. The title is "The aging frontal lobe in health and disease: a structural magnetic resonance imaging study", and you can read the thesis at

http://hdl.handle.net/10616/40977

Brain 101

On Thursday May 24th, Lars-Olof Wahlund, professor at Clinical Geriatrics, Karolinska Institutet, will give a lecture entitled "The Brain for Beginners -- Introduction to neuroscience".

The intended audience are engineers, physicists and other personel who come into contact with anatomical or functional features of the brain but never took anatomy classes, so that they hear terms like "caudatus" and "FTLD" without really knowing their meaning.

The lecture is given at 13.20-15.00 in Kursrum 2 (K64) at Huddinge university hospital. Feel free to download the flyer and invite your colleagues!

Linux for beginners

Given enough interest, there will be a course for absolute beginners in how to use a Linux-based system. You can read more about the contents of the course here:

http://www.smile.ki.se/education/courses/linux_en.html

The course is scheduled for May 22nd at 13-16. Please contact the manager to sign up!

Verify publications

All researchers are kindly requested to verify their publications in the KI/SLL bibliometric database before May 31st. You can find the database here:

https://bibliometrics.ki.se/users/login

Note that address information must also be supplied for a publication in order for it to be properly verified.

Dissertation by Gabriela Spulber

Gabriela Spulber will defend her thesis on Friday 27th of April, at 12.00 noon at the University of Eastern Finland in Kuopio, Finland. The title is "Imaging the progression from mild cognitive impairment to Alzheimer's disease", and you can read more about it here.

SMILE Collaborators page

The SMILE webpage section called "Collaborators" is now in the process of being updated. If you are interested in having your name on this page -- or perhaps a webpage of your own linked to the list on the page -- please contact the manager who will be happy to help you.

You can find the Collaborators page here:
http://www.smile.ki.se/about_us/assoc_en.html
where you also can find examples of different styles of personal pages. 

Summer programming course at PDC

PDC- Center for High-Performance Computing and the KTH School of Computer Science and Communication (CSC) are organizing an introductory course in high-performance computing. The Summer School will be held at the KTH main campus, Stockholm on August 20-31. The course is open to KTH masters students as course number DN2258. Other students, both national and international, as well as academic and industrial, are also welcome to apply. 


This course will give an introduction to the skills needed to utilize high performance computing resources, including an introduction to HPC programming languages, libraries and tools, modern computer architectures, parallel algorithms, and optimization of serial and parallel programs. Case studies in various scientific disciplines will help illustrate these topics. The course consists of both lectures and guided hands-on lab experience. It carries 7.5 ECTS (European Credit Transfer and Accumulation System), where 1.5 ECTS credits are equivalent to one week's workload of 40 hours. The student receives these credits on successful completion of the post-course project. The number of seats are limited. 


The course is suitable for scientist and graduate students with interest in high-performance computing. It requires good experience in programming. The course language is English. 


Course registration opens on March 15, and closes June 1, 2012. 


Read more about the course at http://agenda.albanova.se/conferenceDisplay.py?confId=3301. 

Updated N4U manual

For those interested in applying for a N4U (neuGRID) certificate, there is now an updated version of the how-to! Ask the manager for a copy.

New exam worker

We have a new exam worker in the lab: Dhiraj Kumar, who will be writing his masters' thesis in Machine Learning at Computer Science at KTH here at SMILE. Dhiraj's supervisors are Eric Westman and Carlos Aguliar, and the project is entitled Multivariate comparison of voxel-based versus morphometric analysis. You can read more about it here: http://www.smile.ki.se/education/exam_en.html. 

Matlab updated

The Matlab version in the lab has been updated to release 2012a.

Gabis "spiktårta"

There will be cake in the kitchen of Clinical geriatrics on Tuesday 17^th of April at 15.00, to celebrate the upcoming "spikning" of Gabriela Spulbers thesis (more news on the blog after the spikning).

Matlab learning event

The Matlab learning event scheduled for Wednesday 18^th of April is now full.

Brain Imaging course

The KI graduate student course "Brain Imaging" was held during week 12. All 18 seats were taken and an additional five-six persons listened in without receiving points. We organizers have received generally positive feedback and feel that the reorganization of the course (as compared to 2009 when it was last given) has worked out well.

 

Guests

SMILE has been visited by two guests lately.

Alberto Redolfi, PhD student at Fatebenefratelli Centro San Giovanni di Dio, Laboratory of Epidemiology & Neuroimaging, Brescia, Italy came on two occasions, both in connection with N4U. On the 5^th to 9^th of March he instructed SMILE users in the finer points of using the grid, and on the 21^st to 22^nd of March he did a broad introduction to the grid for the participants in the Brain Imaging course.

Julia Miralbell, PhD student at Department of Psychiatry and psychobiology, University of Barcelona, Spain stayed during the whole Brain Imaging week, from the 19^th to the 23^rd of March, and helped us with the hands-ons for automated volumetry.

Blog problems

The blog is currently not being updated as often as it should. The problem is that the manager’s computer is tied within Atlas to an extremely old version of Explorer, which the blog page no longer accepts as valid. Updates are then made when I’m in the lab, but then I usually have other, more pressing things on my mind. Thus, the dearth of updates lately. IT tells me that they are working on packaging a new version of Explorer which will come out as soon as possible. (This was however a month ago and I have not heard back from them).

New workshop by Rita Almeida

The next workshop on statistical analysis of neuroimaging data by Rita Almeida will be held on Tuesday, 3rd of April from 9.00 to 12.30.

The first 2 hours will be held at the Tellus room, Dept. of Neuroscience, Retzius Väg 8, KI Solna. The last part, the tutorial, will take place in the computer room Space, close to the library at the Solna Campus.

Rita will talk about Bayesian analysis in neuroimaging, with focus on MRI.

The planned schedule follows the same organization as before:

9.00-9.45: "Bayesian methods in neuroimaging"- this first seminar will be an introduction to Bayesian statistics and its applications to neuroimaging.
It is prepared to be a stand-alone overview.

10.00-10.45: " Bayesian methods in neuroimaging - part II", this seminar will focus on more technical aspects and examples.

11.00 - 12.30: Tutorial.

Suggested reading are chapters 22 and 23 of the Statistical parametric mapping book by Friston et al.
http://www.sciencedirect.com/science/book/9780123725608

and the following article:

http://www.ncbi.nlm.nih.gov/pubmed/19059349

Please register by sending the manager an email if you are planning to attend the workshop. In particular, it is helpful to know if you are following the tutorial. The manager will put you in contact with Rita directly.

Here, but busy

There are actually any number of things to blog about: guests, the Brain Imaging course, dissertations that went well... but due to illness and now the demanding task of running the Brain Imaging course there is just no time. Expect a series of posts sometime next week with the details!

Timer functioning again!

Dalkia realized our terrible need for a functioning coffee maker and fixed the broken timer on the power outlet already this afternoon!

Broken coffee maker power outlet

The power outlet in the R43 pentry which is equipped with a timer has broken. There is another outlet without a timer, but please do not connect the coffee machine to that outlet! It is too easy to forget the machine and leave it turned on until it runs dry, breaks down and starts a fire.

Proof in point: this Saturday Leif came by R43 and noticed a bad smell. He found the coffee machine connected to the outlet without a timer, turned on and almost dry. So it is quite possible that there could have been a fire at R43 this weekend, if not for Leif's chance stopping-by!

Dalkia has been notified of the broken outlet and has also been told that we would like to have it fixed ASAP.

Personal entries

The "Collaborators" section of the SMILE webpages is now being updated. As a SMILE user you have the option of an entry on those pages -- ranging anywhere from a mere mention of your name to a full webpage of your own (which will be coded by the manager). You are more then welcome to join the Collaborators page! Please contact the manager for help.

New RSS feed button

I managed to add an RSS feed button to the top of the column to the right of the posts. Now it should be easier for everyone to start following the SMILE blog...!

Dissertation by Lena Cavallin

Lena Cavallin will defend her thesis on Friday 16th of March, at 09.00 in the lecture room C1-87, Karolinska University Hospital, Huddinge. The title is "Reliability of visual assessment of medial temporal lobe atrophy", and you can read the thesis at http://hdl.handle.net/10616/40913

NeuroSynth.org

Here is a link to an interesting project: NeuroSynth.org. It is an open source project which extracts fMRI data from published articles and visualizes the meta-analysis. It is also possible to select specific regions in the human brain and view associated terms.

Re-scheduling of talk

The talk by Raffaella Crinelli has now been rescheduled to take place on Thursday 29th of March at 13.00, in the R43 conference room.

Tomorrow's talk cancelled

Tomorrow's talk by Raffaella Crinelli has been cancelled due to illness.

PACS machine upgrade

Due to Atlas, the PACS machine in the lab needs to be upgraded. That however also means that we cannot run any external software such as Statistica on it. Therefore, an ordinary Windows machine will be bought for the lab for this type of software.

Spring guests

SMILE will have several visits during the spring:

5th-9th of March: Alberto Redolfi (PhD student at Fatebenefratelli Centro San Giovanni di Dio, Laboratory of Epidemiology & Neuroimaging, Brescia, Italy). He will work with Gabi on the N4U project.

19th-23rd of March: Julia Miralbell (PhD student at Department of Psychiatry and psychobiology, University of Barcelona, Spain). Julia is back once again! This time for the Brain Imaging course, to which also Alberto will return for a few days.

2nd of May to 21st of December: Daniel Ferreira Padilla (PhD student at Psychobiology and Methodology Department, Faculty of Psychology, University of La Laguna, Tenerife, Spain). Dani is also returning to us for a really prolonged stay.

Upcoming: Matlab and Linux

We now have dates for the Matlab and Linux mini-courses: 18th of April and 22nd of May respectively. Sign up now!

AD symposium in Stockholm

You may be interested in the Stockholm/Springfield Symposium on Advances in Alzheimer Therapy which takes place on May 9-12 in Stockholm. Note that the deadline for abstracts is already on the 15th of February!

obelix has moved

The new server room at nuclear medicine is now operational, and obelix has been moved there. It is reachable as before from the Imagelab computers, but if you have your own setup you need to change the IP number of obelix. Contact the manager to get the new IP!

The result: Silence of the lab...

Eco-friendly power save

Just a reminder: the screens in the lab should be switched off when no-one is using them. This will generate less heat in the lab and waste less energy. Make it a rule to think "Did I turn off the screens?" before you leave the lab...!

Rebooting freja

In order to keep freja healthy we have decided to reboot it at regular intervals. For starters we will do it once per month, on the first Monday of the month. These are the dates: 5th of March, 2nd of April, 7th of May, 4th of June and 2nd of July.

6th Kuopio Alzheimer Symposium

News about the 6th Kuopio Alzheimer Symposium, which will be held in Technopolis, Kuopio, Finland, June 14-16, 2012.

6th Kuopio Alzheimer Symposium will feature an advanced scientific program with new results concerning early diagnosis, new advances in brain imaging,
biomarkers for AD, search for drug targets, prevention, and treatment and care. The program also includes a Finnish Session "Memory Day" targeted for
nurses and other personnel working with memory patients.

For more details, click
www.uef.fi/kuopioadsymposium

Note that abstract submission deadline is by April 30, and registration by May 31.

Compressed sensing starts 6/2

Some further information about when the KTH course in Compressed sensing starts and where the lectures are given.

The course starts on Monday Febr. 6 at 15:15 and the lectures are given in seminar room 3733, Lindstedtsvägen 25, floor 7. The webpage of the course is

http://www.math.kth.se/~jostromb/KURSER/Forskarkurs_Compressed_Sensing/.

Statistica course

When describing the spring course plan at SMILE earlier, I forgot to mention that we during the spring also plan to hold an introduction to Statistica -- how to run the program (not to statistics in general). Further information later on.

Move of obelix

The Hermes server obelix will be moved to a new, more computer-friendly environment on floor six at some point in the near future. The server will during the move be turned off for a couple of hours, and the IP-number will change. If you are performing work on obelix and need to know exactly when the move will happen, contact me.

Additional talk

A talk has been added to the spring list of presentations:

Monday 13th of February (note the unusual day of the week):

Olga Voevodskaya (Exam work presentation for the Master’s degree in Engineering Physics at KTH):

The reliability of GABA measurements in the human brain by MRS at 3T

Upcoming courses

In the lab we aim for the following this spring:

Matlab for beginners -- planned for April
Linux for beginners -- planned for May

Additionally, a course in Compressed sensing and sparse signal processing will be given at KTH in February. Read more here.

Outcome of Atlas meeting

Today I attended the last Atlas meeting for medical physics. However, I did not become much wiser as to when the 15-net will be transformed to a pure server-net and our Imagelab machines will have to switch IP-numbers -- they didn't know. What was discovered though was that the PACS machine in the lab seems to have been forgotten by the X-ray department, but this will now soon be taken care of (I will be notified of when). After that, you cannot log on to the PACS machine if you do not have an HSA-ID. The manager can help getting you a HSA-ID if you do not have one.

Upcoming conferences of interest

These upcoming conferences may be of interest:

Congress of Neuropsychopharmacology: 3-7 June, Stockholm (http://www.cinp2012.com). Deadline for abstracts 31/1.

Alzheimer’s Association International Conference: 14-19 July, Vancouver(http://www.alz.org/aaic). Deadline for abstracts 30/1.

Human Brain Mapping: 10-14 June, Beijing (http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3458)

2012 spring talks

The spring talk academical calendar is as follows:

Thursday 26th of January:
Tomas Jonsson (PhD student at Department of Clinical Science, Intervention and Technology at Karolinska Institutet):
Characterization of the BOLD signal in functional MRI

Thursday 9th of February:
Farshad Falahati Asrami (Exam work presentation for the Master’s degree in Biomedical Engineering at Linköping university):
Alzheimer's Disease Classification using K-OPLS and MRI

Thursday 23rd of February:
Raffaella Crinelli (PhD student at Department of Neurobiology, Care Sciences and Society at Karolinska Institutet):
TBD

Thursday 15th of March:
Erika Jonsson Laukka (PhD at Aging Research Center and Department of Neurobiology, Care Sciences and Society at Karolinska Institutet):
Genetic effects on old-age cognitive functioning – a report from the population-based SNAC-K study

Thursday 26th of April:
Gareth Morgan (Senior lecturer at Department of Pathology, Karolinska University Hospital):
Microscopic image analysis in pathology

Thursday 31st of May:
Babak Hooshmand (PhD student at Aging Research Center and KI Alzheimer’s Disease Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet):
Folate, vitamin B12, and vitamin D in relation to cognitive performance and structural brain changes

Users' meetings

The first users' meeting of the spring has been held, and the minutes will shortly be available at the SMILE webpages (and be sent to the mailing list). The set dates for the spring users' meetings are:

14/2, 13/3, 10/4, 8/5 and 5/6.

Dissertation by Tomas Jonsson

Tomas Jonsson will defend his thesis on Friday 10th of February, at 09.00 in the lecture room C1-87, Karolinska University Hospital, Huddinge. The title is "A Characterization of the BOLD signal in functional MRI", and you can read the thesis at http://hdl.handle.net/10616/40882

All are welcome!

E-prime

E-prime 2.0 by Psychology Software Tools, a program designed to facilitate the conception of any experiment that uses a computer as an interface between the subject and the experimenter, has now been installed on the PACS machine.

Users' meeting tomorrow

Tomorrow at 10 o'clock the first users' meeting of the spring term will be held in the R43 conference room. Note the time -- we are now implementing the change to an earlier time slot which was decided on at the last meeting. Hope to see you all there!