SMILE Imagelab

Statistica course

2012-01-26T13:41:00.002+01:00

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

2012-01-25T15:11:00.003+01:00

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

2012-01-25T15:03:00.003+01:00

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

2012-01-25T14:58:00.002+01:00

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

2012-01-19T16:17:00.003+01:00

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

2012-01-19T16:00:00.001+01:00

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

2012-01-19T15:54:00.003+01:00

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

2012-01-19T15:51:00.003+01:00

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

2012-01-19T15:48:00.000+01:00

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

2012-01-16T13:48:00.000+01:00

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

2012-01-16T12:54:00.001+01:00

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!

New coffee maker

2011-12-28T15:14:00.001+01:00

We hava new coffee machine in the pentry, replacing the one for which the glass pot was broken.

Merry Christmas!

2011-12-22T15:32:00.002+01:00

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

Access to the webpages

2011-12-15T14:58:00.000+01:00

Finally the Atlas problem has been solved, so that I can update the SMILE webpages again...! What a relief!

Printing

2011-12-13T13:34:00.002+01:00

Printing in the lab was suspended yesterday because of Atlas. I have now gotten hold of a sympathetic person who has reset the printer IP to its original state, so printing is now again possible. Still no handle on when the IP switch from the 15-net will be made, though.

Atlas again

2011-12-06T13:16:00.002+01:00

There will be some disruptions in net access for units on the "15-net" (i.e. those machines with IP-number 10.48.15.xxx -- basically all the machines in the lab) tomorrow Wednesday between 15-16. This may be connected to the moving of medical physics at R43 to Atlas which also will take place tomorrow.

Fokus Flemingsberg

2011-12-05T16:17:00.002+01:00

The latest issue of the newsletter "Fokus Flemingsberg" has the theme "Medical technology" and runs a piece on the KTH donation. You can find the issue online here:

http://www.flemingsberg.se/sv/Nyheter/Fokus-Flemingsberg/

(in Swedish only) -- look to page 4-6 for an interview with Peter Aspelin and Gabriela Spulber.

neuGRID certificates

2011-12-05T16:14:00.003+01:00

We have now received certificates for most of those interested in experimenting with running neuGRID, and have had our first "try-it-out"-session. If you are interested in getting a certificate so that you can join us, please contact the manager! In case of enough interest I can also schedule another half-day (or shorter) neuGRID introduction in case you aren't quite familiar with what it is...

Workshop on statistical analysis of neuroimaging data

2011-12-05T14:11:00.002+01:00

Rita Almeida is continuing the workshop series over in Solna. The next workshop on statistical analysis of neuroimaging data will be held on Thursday the 15th of December from 13.00 to 16.00. The first 2 hours will be held at a room to be announced at the Solna campus of KI, and the last part, the tutorial, will take place in the computer room Enter, close to the library at the Solna Campus.

Rita will talk about experimental design for neuroimaging, with focus on fMRI. The planned schedule follows the same organization as before:

13.00-13.45: "Experimental design for functional neuroimaging"- this first seminar will be an introduction to experimental design with focus on functional magnetic resonance imaging and analysis using the general linear model. It is prepared to be a stand-alone overview.

14.00-14.45: " Experimental design for functional neuroimaging - part II", this seminar will focus on more technical aspects and examples.15.00 - 16.00: Tutorial. Suggested reading are chapters 13 and 15 of the Statistical parametric mapping book by Friston et al. http://www.sciencedirect.com/science/book/9780123725608

Please contact the manager to sign up for the workshop!

Atlas is arriving

2011-12-01T08:55:00.001+01:00

The Karolinska hospital is changing its computer system to the Atlas set-up. This means that many computers are locked down and cannot be administrated as before (including the manager's own desktop PC which was changed last week and from which I for the moment cannot print or update the SMILE webpages).

The computers at SMILE will not be touched (with one exception) but changes around SMILE will still affect us -- so that sometime next week all IP numbers to the lab computers will change (I have not been given information about the exact date or what the new numbers will be). We can probably expect other glitches as well.

The only computer in the lab to be touched by Atlas is the PACS computer. I have not been given information on when this will happen, but I expect it to be soon (certainly before Christmas). I strongly recommend all users who have data on the desktop or file system of the PACS computer to back it up securely, as soon as possible!

Workshop on statistical analysis of neuroimaging data

2011-10-24T15:35:00.002+02:00

There will be a workshop on statistical analysis of neuroimaging data held by Rita Almeida (the second part in a series). It will be held on Tuesday the 15th of November at the Tellus room, Dept. of Neuroscience, Retzius Väg 8, KI Solna, from 9.00 to 12.30.

The workshop will continue with the general linear model analysis, discussing group analyses and corrections for multiple comparisons.The planned schedule follows the same organization as before:
9.00-9.50: "Statistical inference on functional neuroimaging data: group analyses and corrections for multiple comparisons" - this first seminar will be an introduction to both group analyses and the problem of multiple-comparisons in the analysis of neuroimaging data, with emphasis on fMRI data. It is prepared to be a stand-alone overview.
10.00-10.50: "Statistical inference on functional neuroimaging data: group analysis and corrections for multiple comparisons- part II", will focus on more technical aspects of inference on neuroimaging data.
11.00 - 12.30: Tutorial. If there are people interested we can go over the tutorial of the previous session too.

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, since that requires some practical arrangements.)

Bamboo pen missing

2011-10-05T13:28:00.002+02:00

The special drawing pen that belongs to one of the black Bamboo drawing tablets in the lab has gone missing. The tablet itself was missing until recently, when it was found on the white bench outside the lab.

The tablet will not work without the pen, so if you have seen it, please tell the manager! The pen is not useful in itself and comes with a small charging station to store it in.

Talk moved

2011-09-29T12:35:00.001+02:00

Today's talk "Microscopic image analysis in pathology" by Gareth Morgan has been postponed until a later date.

New talk

2011-09-22T13:42:00.002+02:00

A new talk -- an exam work presentation -- has been added to the seminar list.

Thursday 13th of October: Mahsa Fatahi (Exam work presentation for the Master’s degree in Medical Imaging at KTH):

Progression of Multiple Sclerosis related atrophy, evaluated by MRI based FSL volumetric method

It will take place at 11.00 in the R43 conference room (as always).

Nobel forum halfday

2011-09-22T13:00:00.002+02:00

There will be an interesting halfday Nobel forum workshop entitled "Neuronal network function in normal aging and Alzheimer´s disease" on October 6th (register before Spetember 30th). Read more on the
KI webpage.

2011 autumn talks

2011-09-20T14:58:00.002+02:00

Finally the schedule for the autumn's talks has been finalised!

Thursday 29th of September:
Gareth Morgan (Senior lecturer at Department of Pathology, Karolinska University Hospital):
Microscopic image analysis in pathology

Thursday 20th of October:
Yanlu Wang (PhD student at Department of Clinical Science, Intervention and Technology at Karolinska Institutet):
Functional Network Identification in Human Resting-state fMRI using Hierarchical Clustering by Time-Lagged Correlations

Thursday 27th of October:
Virginija Karrenbauer (PhD student at Department of clinical neuroscience at Karolinska Institutet) and collaborators:
Comparison of MRI lesion location in multiple sclerosis patients with and without oligoclonal bands in the cerebrospinal fluid

Thursday 24th of November:
Babak Hooshmand (PhD student at Aging Research Center and KI Alzheimer’s Disease Research Center, Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet):
The impact of homocysteine and B vitamins on Alzheimer's disease, cognitive performance, and structural brain changes

Thursday 15th of December:
Carl-Henrik Ehrenkrona (student at Department of Psychology, Karolinska University Hospital): Atrophy, reserve and compensation:
A tentative framework for understanding brain-cognition relationships in aging. Preliminary results from the SNAC-K project

Dissertation by Michael Schöll

2011-09-19T14:12:00.002+02:00

Michael Schöll will defend his thesis on Friday 7th of October, at 09.30 in the lecture room 9Q Månen, Karolinska University Hospital, Huddinge. The title is "A Multi-tracer PET approach to study early-onset familial and sporadic Alzheimer's disease", and you can read the thesis at http://hdl.handle.net/10616/40696

All are welcome!

Dissertation by Gunnar Herlin

2011-09-15T11:27:00.001+02:00

Gunnar Herlin will defend his thesis on Friday 23rd of September, at 09.00 in the lecture room C1-87, Karolinska University Hospital, Huddinge. The title is "Nuclear medicine imaging of lung cancer and esophagus cancer", and you can read the thesis at http://hdl.handle.net/10616/40609.

All are welcome!

New exam work available!

2011-09-14T11:05:00.002+02:00

We can offer a new exam work opportunity in Stefan Brené's group at the Experimental MR unit at KERIC, Karolinska University Hospital in Solna (see http://expmr.ki.se/). The work consists of data analysis of pharmacological MRI rat experiments on the 9.4 T animal camera. A suitable background includes knowledge in MATLAB programming and statistical evaluation.

For more information, please contact Peter Damberg or Stefan Brené (ask the manager for their contact details).

Dissertation by Johanna Öberg

2011-09-13T10:34:00.002+02:00

Johanna Öberg will defend her thesis on Friday 30th of September, at 09.00 in Hörsalen, NOVUM, floor 4, KI Campus Huddinge. The title is "Multivariate data analysis applied to MRS and MRI studies of aging and spinal cord injury", and you can read the thesis at http://hdl.handle.net/10616/40701.

All are welcome!

New exam workers

2011-09-13T10:22:00.003+02:00

We have two new exam workers in the lab:

Olga Voevodskaia from KTH will work with Tie and Martin on a thesis about the reliability of GABA measurements using MRS

Farshad Asrami from Linköping University is supervised by Eric and Carlos on a project for AD classification using multivariate analysis

Welcome!

Donation to KTH

2011-09-08T11:18:00.002+02:00

One of the largest private donations ever made to KTH (70 million SEK) will be used to create a new center in image analysis, and SLL is at the same time creating a new professorship to be situated at the center. The center will strengthen the collaboration between Karolinska Institutet, the university hospital and KTH.

You can read more about the donation and the center in Dagens Medicin (in Swedish) here and here.

SMILE is represented in the center development group by Peter Aspelin and Eva.

Brain Power meeting

2011-09-08T11:15:00.001+02:00

This year's Brain Power meeting will take place on September 29-30. SMILE will be represented by Carlos (who will give a talk), Olof (who will show a poster), Eric and Lars-Olof.

Yet another postdoc position

2011-09-08T11:12:00.000+02:00

From professor Metin Gurcan (whom some of you may remember from his visit here last summer) has sent me a flyer for an open postdoc position in medical image analysis at his home lab The Clinical Image Analysis Laboratory, Department of Biomedical Informatics, Ohio State University, USA. Deadline 28/10. Read more on the SMILE webpages!

neuGRID success

2011-09-05T11:00:00.001+02:00

neuGRID has been listed on the EU:s Research infrastructure Success stories homepage. See it all here:

http://ec.europa.eu/research/infrastructures/index_en.cfm?pg=success4

One more postdoc position

2011-09-02T14:38:00.000+02:00

You can find the call for an open post-doc position in Clinical neuroscience and neuroimaging with focus on studies of cerebral changes related to chronic psychosocial stress at KI on the SMILE webpages. Deadline 30/9.

Postdoc position

2011-09-02T11:30:00.002+02:00

You can find the call for an open post-doc position in fMRI at Stress Research Institute on the SMILE webpages. Deadline 15/9.

Exam work project wanted

2011-08-31T16:30:00.001+02:00

A talented person from the Computer Simulation for Science and Engineering program at KTH is looking for an exam work project. If you have a project available which involves programming and medical visualization, please contact the manager for a CV of the student and more information.

New Statistica courses

2011-08-31T16:27:00.002+02:00

Statistica courses will be held again by Statsoft, as every autumn (and spring).

This term there will be no courses in Huddinge, but there are two opportunities in Solna: October 25-28 (block 1+2) and December 6-9 (block 1+2). See the flyer on the noticeboard in the lab for more details, or ask the manager.

Next users' meeting

2011-08-31T16:26:00.001+02:00

Note that the start of the autumn also means that the users' meetings will start up again. The next one is on Tuesday 6th of September at 11.00 in the R43 conference room.

First autumn seminar

2011-08-31T16:24:00.001+02:00

The autumn's first seminar will be given on Friday (2/9, not Friday not Thursday!).

Soheil Damangir (Exam work presentation for the Master’s degree in System Control and Robotics at KTH): Fully Automatic Segmentation of White Matter Lesions

Iranian collaboration

2011-08-04T11:15:00.001+02:00

The lab has been contacted by an Iranian PhD student who is interested in finding a collaboration in MRI imaging. He has previously worked on cine cardiac MRI. Please contact me to get his resume and a couple of articles!

Log out of Matlab, please

2011-08-04T11:14:00.000+02:00

A note to those who use Matlab: please exit the program when leaving freja (even if you do not log out of freja itself), since the license otherwise is tied up and unavailable to other users!

New SMILE email list address

2011-08-04T10:50:00.001+02:00

The SMILE emailing list address will very soon change. You need to change any eamil program filters you may have set up and enter the new email address in your address book.

I will not give out the list address here for spam reasons -- if you haven't received the new list address in the email, send me a message to get it.

Open exam work project

2011-08-01T11:15:00.001+02:00

We have a new exam work project coming up in the lab, open for application. Read more here:

http://www.smile.ki.se/education/exam_en.html

New cooling unit

2011-07-11T15:03:00.003+02:00

Well! As soon as I wrote a post about the ventilation not working, Dalkia showed up to fix it. (Do they read this blog? Or was it the fact that I called almost every day during the last two weeks to ask when they were coming? (Alerting them to the problem about a month ago)). We now have a new cooling unit in the lab. Please be friendly to it.

Vacation

2011-07-11T09:27:00.002+02:00

The manager will be on vacation week 29-30.

Valhall is not feeling well

2011-07-11T09:22:00.002+02:00

I noticed on Thursday that valhall is not responding. This is very worrisome! Strangely enough, no disk displays a warning message (though the system itself warns for a faulty disk). We will look further into this as soon as possible. The new ethernet unit yggdrasil has just arrived at the lab, but it will not be started until the ventilation is fixed.

Hermes service

2011-07-11T09:10:00.000+02:00

Hermes has announced that they will come and do the yearly service and maintenance on the Hermes machines already today, Monday 11th.

No ventilation

2011-07-11T09:06:00.002+02:00

The cooling unit in the lab has broken down (already several weeks ago). I have been trying and trying to get Dalkia to come and install a replacement unit (it is extremely frustrating dealing with the slow workings of maintenance at the hospital at times like these!) Hopefully I will succeed soon... but be prepared that the lab at the moment is very hot.

Talk tomorrow!

2011-06-21T15:20:00.000+02:00

We have an extra talk in the seminar series on very short notice. Tomorrow Wednesday 22:nd of June at 09.30 in the R43 conference room there will be the exam work presentation by Daniel Thor from medical physics. Note that the presentation will be given in Swedish!

The title of the talk is "Quantification of myocardial perfusion rest-stress change in SPECT -- without the use of normal templates".

All are welcome!

The end of the GSK project

2011-06-21T14:39:00.002+02:00

The Imagelab collaboration with GlaxoSmithKline has now been completed, and our role as data collection center is finished.

Excerpts from the letter from GSK:

The last subject participating in the study completed examination on the 30th of May 2011. The overall safety profile of the compound remains favorable, no new microbleeds have been reported from any subjects on active treatment and no cases of vasogenic edema have been reported. [...] I hope that you agree with us, saying that it has been an interesting and challenging study for us all.

On behalf of the BA study team we would like to thank you all for your valuable support around the phase I program of our compound. We couldn’t have achieved this important milestone without your important engagement, and contribution. It has been a pleasure and privilege to work with you all.

All the best
For the BA study team

Pia Lisjö
Global Study Manager

More on the SSBA summer school on image registration

2011-06-13T13:51:00.001+02:00

The Medical Informatics group at Linköping University will arrange this year's SSBA Summer School on Image Registration, between 29th of August and 2nd September 2011.

There is now an update with practical information here:

http://www.imt.liu.se/mi/summerschool2011/index.html

Note that the deadline for registration is June 30th!

Vacation

2011-05-31T15:23:00.002+02:00

The manager will be gone on vacation during June 1-8, back on the 9th. Sorry for the short notice, but the manager is currently at home with a cold. (Therefore the manager will go on vacation with a horrible runny nose and persistent cough...)

MR basics, again

2011-05-23T11:05:00.001+02:00

There will be one more MR basics lecture by Love Nordin. It will be given on Tuesday 31st of May at 14.30 in the R43 conference room, and it is already almost full. There are still a few seats left -- in case of interest, contact me!

New seminar

2011-05-23T11:04:00.001+02:00

As previously announced, Tomas Jonsson will give a seminar. This will take place on June 14th at 11.00 in the R43 conference room and has the title News from the 2011 ISMRM conference . All are welcome!

Cancelled seminar

2011-05-19T10:37:00.000+02:00

Virginija Karrenbauer has unfortunately needed to cancel her talk which should have taken place today at 11. We hope to see Virginija here during the autumn instead.

Even though there is no seminar today, the seminar series is not yet over for the summer. We will have a seminar next week (by Lena Cavallin, I will send a reminder later), and also an extra seminar by Tomas Jonsson on the news from the ISMRM conference, on a date to be decided.

The Hermes situation

2011-05-10T10:12:00.002+02:00

(See the previous entry about Hermes first).

At the board meeting it was decided to keep the HERMES computers and not to remove HERMES. Users can use those computers and can ask the manager to install other softwares on them if they want to.

neuGRID introduction on Wednesday 18th of May

2011-05-10T10:04:00.002+02:00

I realize I have forgotten to put up information about the neuGRID introduction on Wednesday 18th of May here on the blog!

neuGRID supplies the individual researcher with powerful computational resources, sophisticated algorithms with which to process brain images, and database access -- all within easy reach from the personal laptop (you can read more about neuGRID on our dedicated neuGRID web page).

The neuGRID event will take place on the 18th of May at 13-16 in the X-ray department's library in Huddinge (C2-42). All are welcome!

We will cover the following aspects:

What is neuGRID? (13-14)
- What is a grid?
- How to create a certificate
- Overview of the functionalities inside neuGRID
The LONI pipeline tool (14-15)
Creating scripts with gLite (15-16)

Autumn's users' meetings

2011-05-10T10:03:00.002+02:00

I know it's early, but here are the dates for the users' meetings during the autumn: 6/9, 4/10, 1/11 and 6/12.

Cancelled users' meeting

2011-05-05T12:10:00.002+02:00

The June users' meeting has been cancelled. We will next meet on September 6th.

Moved users' meetings

2011-05-05T10:45:00.003+02:00

The May meeting has been moved from 3rd of May to 5th of May (due to the lectures on the 3rd).

MRI and PET lectures at Novum on May 3rd

2011-04-28T14:19:00.001+02:00

The division of Alzheimer Neurobiology Center are arranging the PhD course "Application of molecular biology and molecular brain imaging techniques in neurodegenerative disorders" from 2nd May – 12th May, 2011.

On May 3rd there will be two public talks:

9:00-10:45

"Introduction of MRI imaging technique and application in
neuro-degenerative diseases".

Elna-Marie Larsson, professor, överläkare
BFC/Röntgen
Akademiska Hospitqal, Uppsala

11:00-12.15

"Development of PET tracers and use of PET in neurodegenerative diseases".

Bengt Långström, Professor
Uppsala University,
Department of Biochemistry and Organic Chemistry
Faculty of Technology and Science, Uppsala, SWEDEN

Place: Seminar room in Geriatric-lab, Novum 4th floor

Kuopio workshops

2011-04-28T14:09:00.002+02:00

Two workshops are organized in Kuopio on June 13-15:

14th Bio-NMR Workshop (MRI of stroke, epilepsy
and neurodegenerative diseases)

PredictAD workshop

Venue: University of Eastern Finland, Mediteknia Auditorium, Kuopio, Finland.

Organizers: Biomedical Imaging Unit, A.I. Virtanen Institute for
Molecular Sciences, Graduate School of Molecular Medicine, and
Institute of Clinical Medicine, Neurology, University of Eastern Finland

These workshops will cover topics from basic principles of MRI
techniques to applications in studies of neurodegenerative diseases
and finally to clinical studies. The aim is to bring together
international renowned faculty of MRI researchers from both
experimental and clinical research environment.

Please, register by May 31, 2011. (Deadline for Abstracts is May 15, 2011.)

New seminar on 19th of May

2011-04-27T11:50:00.001+02:00

We will have an extra seminar in the academic meeting series on Thursday 19th of May, at 11.00 in the R43 conference room.

Virginija Karrenbauer (PhD student at Department of clinical neuroscience at Karolinska Institutet) and collaborators:

Comparison of MRI lesion location in multiple sclerosis patients with and without oligoclonal bands in the cerebrospinal fluid

All are welcome!

Change of title

2011-04-20T16:14:00.001+02:00

Tomorrow's seminar by Xiaozhen Li has a new title:

"Pre-processing of resting-state fMRI".

ISMRM 2011

2011-04-13T09:09:00.001+02:00

The ISMRM meeting will this year be held on May 7-13 in Montreal, Canada. Participants going from the lab include Tomas Jonsson, Love Nordin and Martin Uppman. We hope to hear a report from them when they get back on their impressions of what's new!

Goodbye to Ariadna

2011-04-12T10:36:00.002+02:00

Ariadna is on her way back to Spain after her two month stay here at SMILE. We will therefore all go out to dinner tomorrow Wednesday, at 19.30 at the Vapiano by Stureplan. All are welcome!

Summer school on image registration

2011-04-11T13:00:00.001+02:00

The Medical Informatics group at Linköping University will arrange this year's SSBA Summer School on Image Registration, between 29th of August and 2nd September 2011.

You can find more information here:

http://www.imt.liu.se/mi/summerschool2011/index.html

N4U passed!

2011-04-06T16:57:00.003+02:00

The N4U application for the continuation of neuGRID (to actually make the structure user-friendly) has been approved by the EU! Perhaps the project will even start as early as this coming autumn, believe it or not.

Hermes

2011-04-06T15:43:00.001+02:00

At the Hermes meeting the present users unanimously voted to stop using Hermes and instead replace it with other freeware. The issue will be brought to the board at the next meeting on the 14th.

Brain Imaging course

2011-04-06T15:34:00.002+02:00

SMILE will give the Brain Imaging course again (you can find the schedule from last time here), but not this year. We are aiming for the next-to-last week of March next year. More information closer to the event...

Formal consent for PACS

2011-04-06T15:26:00.002+02:00

From now on, you need to have formal consent by the head of the radiology department for your specific project if you are using PACS data. Write a short description of your project and what data you would like to use and attach your contact address, email etc. Send this to the manager who will help you put it together into a consent form!

Cancelled talk

2011-04-05T14:07:00.000+02:00

The talk by Inge van der Kroon on Thursday 14th of April is cancelled.

Workshop on support vector machines by KI's Rita Almeida

2011-04-04T16:04:00.001+02:00

A workshop on support vector machines will be held by the statistician Rita Almeida, organized by Tim Ziermans in Torkel Klingberg's group.

When: 14th April, 9.00-12.00
Where: KI, Dept. of Neuroscience, Retzius Väg 8 (room to be determined)
Who: Anyone interested
Costs: None

The 1st hour Rita will provide an overview of 'Multivariate pattern classification for neuroimaging' with a focus on fMRI. The 2nd hour will be a lecture on 'Applications of multivariate pattern classification' . Depending on the number of participants the 3rd hour will consist of a hands on tutorial (software will be provided beforehand).

For those interested in participating, please send an email to Tim Ziermans (tim.ziermans@ki.se)!

New dishwasher

2011-04-04T14:28:00.002+02:00

A new dishwasher has arrived and was installed in the R43 kitchen on Friday. So now you can put your dirty mugs and plates in the dishwasher in the familiar way again!

Welcome back Julia!

2011-04-04T14:23:00.002+02:00

We welcome back Julia Miralbell from the Department of Psychiatry and psychobiology at the University of Barcelona in Spain. She will be visiting us until the 1st of July. Great to see you back here, Julia!

New stapler

2011-04-04T14:21:00.001+02:00

The lab has acquired a new stapler of a similar type to the one in the X-ray office. Now we don't need to bother the X-ray guys anymore but can do our own multi-article-power-stapling!

More memory in freja

2011-03-31T13:59:00.002+02:00

The memory in freja has been expanded from 4 GB to 16 GB, which will increase the capabilities of the computer from now on!

AstraZeneca MR meeting

2011-03-30T08:59:00.001+02:00

On Friday, the R43 conference room is booked from 13.00 for a meeting on experimental MR with participants from Solna, ARC and AstraZeneca. I will give a short presentation on the structure of SMILE, but there are other talks scheduled as well. Meeting attendance is closed, but if you are really interested, contact me and I'll find out if there is room for one more.

Broken dishwasher

2011-03-28T14:29:00.001+02:00

The dishwasher in the R43 conference room is broken! Water leaks out. A new machine has been ordered -- until then, please clean your dishes by hand!

Update on seminars

2011-03-22T11:21:00.002+01:00

The seminar by Anna Gärdin on Thursday 31st of March is moved to 15.00.

The seminar by Ariadna Besga on Thursday 7th of April has been cancelled.

The title of Inge van der Kroon's talk on Thursday 14th of April is "CT and MRI brain tissue fractions, what is it what we really get".

Welcome!

HERMES meeting

2011-03-21T14:07:00.003+01:00

Since the HERMES machines in the lab work in an increasingly erratic manner, we need to make a decision on whether we want to continue supporting the HERMES system or if we want to replace the functionalities we use in HERMES with other software.

In order to discuss this, we will have a meeting on Tuesday 5th of April at 10.00 in the R43 conference room (just before the ordinary users' meeting at 11.00). If you are interested in the future of HERMES in the Imagelab I hope you can attend this meeting! In order to prepare for the meeting, please think about what functions you use inside HERMES and if you know any other software which could be used instead (such as ITK-SNAP for manual tracing).

Statistica on Youtube

2011-03-21T14:05:00.002+01:00

You can now find some neat introductory movies on how to use Statistica on Youtube:

http://www.youtube.com/user/StatSoft#g/c/CF3388C47AFF8365

Statistica is installed on the new PACS-machine in the lab.

MR basics lecture

2011-03-17T09:18:00.003+01:00

The date for the MR basics lecture has now been set. It will be given by Love Nordin on Wednesday 27th of April at 10.30 in the R43 conference room. There is still one seat free! The lecture is part of the MR "driver's license" and will count towards the license.

Linux mini-course

2011-03-17T09:16:00.002+01:00

The date for the Linux mini-course has now been set. It will be given on Tuesday 19th of April at 13.00 in the R43 conference room. There are still two seats free for interested participants!

N4U

2011-03-17T09:09:00.002+01:00

The neuGRID consortium (plus some new partners) handed a while ago in an application to the EU FP7 programme for a continuation of the neuGRID project called neuGRID for you (N4U). The evaluation summary report was made official yesterday, with very high scores... (no guarantee of funding though, but looking good!)

Going to Brussels

2011-03-17T09:08:00.000+01:00

The manager will be going to Brussels on 23rd-25th of March, to be present at the EU Final review of the neuGRID project (where the success of the project is evaluated and the accounting gone over).

Moved users' meeting

2011-03-08T10:09:00.002+01:00

The users' meeting today has been moved to next week (15th of March) since many regular users are attending the AD/PD conference in Barcelona this week.

Lecture on brain pathology

2011-03-08T09:38:00.002+01:00

On Monday 14th of March there will be a one hour lecture on brain pathology, given by Lena Cavallin. It will take place in the X-ray lecture room at C2-42 at 13-14. All are welcome, no sign-up is needed and you are free to spread the information to anyone you think might be interested!

Last neuGRID meeting

2011-03-07T17:03:00.003+01:00

The manager will be in Brussels during 23-25th of March to participate in the EU Final Review of the neuGRID project, which then will be officially closed. The grid itself is very much alive however, and we plan on holding learning events during the spring on how to use it.

Cards under control again

2011-03-07T17:01:00.002+01:00

The business of creating new cards and giving access to existing cards has now been sorted out. If you cannot enter SMILE, contact the manager who will send you information on how to proceed.

Card panic!

2011-02-28T17:00:00.002+01:00

As has been announced last summer (see e.g. this blog entry) the hospital is upgrading its entrance systems. The change was originally scheduled to take place last autumn, but delays have postponed the new card reader installation at R43 until this spring.

Today, completely out of the blue without any advance notice, the new card readers were installed. This means that your cards do not open the R43 corridor or the SMILE door anymore. I have been expecting the arrival of instructions from the security department on how to deal with upgrading your cards, but have not received any. I am struggling to find out how to do it, but important people at the security department are ill and I have not been able to solve this yet.

How difficult it will be to upgrade your card depends on where you work and other things.

* If you are hired by Karolinska Hospital and have a Swedish personal number you probably already have a SIS-marked card. All you need to do then is to contact me and give me some details such as your personal number. I can then send an email and your card will probably work almost at once.

* If you are hired by the hospital but do not have a Swedish personal number you will have to get an OSIS card. I'm not sure how to order those yet.

* If you are not hired by the hospital but need access to PACS, TakeCare or other hospital computer systems you also need to have an OSIS card.

* I think this goes for most of you: if you are not hired by Karolinska Hospital and do not need to have access to PACS etc, but just want to be able to open the doors, you will need to have a K-badge. I also do not know how to order K-badges, but I'm sure that you will need to have your photo taken by the hospital photographer in the process.

I will hopefully find out how these things work within a few days. Meanwhile, I want to start collecting information from those of you who wish to renew your access to the SMILE doors.

All those who want to be able to open both SMILE doors, please contact me ASAP. I will then ask you for the details I think are needed from you in order to get you renewed access.

To try and minimize the bother for the physicists with offices close to the entrance door, please call me on 08-585 848 07 when you are standing outside the R43 corridor door and I will come and open it for you.

PACS is here

2011-02-22T10:19:00.003+01:00

The new PACS machine has arrived! I will be working on installing most of the programs we had on the old machine on it, but the licenses for Brain Voyager and IDL have expired. We will probably not get IDL again, and I'd like you to tell me if you are interested in having access to Brain Voyager as we may choose not to renew that license either.

As said earlier, the old machine has been removed. If you urgently find that you have forgotten to back-up important files on it, I can still get hold of the technician who took it away -- he hsa promised to keep it for a few weeks before getting rid of it.

Update on freja connections

2011-02-18T18:21:00.004+01:00

The dicom server installed on freja is now the dcm4chee toolkit. We are looking at the possibility to set up a connection to the PACS as we had earlier. An advantage of the dcm4chee toolkit is that you can ask to have a username and then can log on a webservice to immediately see that your data has been safely stored on it.

Working from home

2011-02-18T18:19:00.001+01:00

Please note that the manager will be working from home on Fridays for the foreseeable future.

New PACS machine

2011-02-18T18:18:00.000+01:00

The new PACS machine will be arriving soon at the lab -- on Monday 21st of February already! The technician installing the new PACS machine will remove the old computer, so if you have any files that you need to save on the old machine, please do so as soon as possible.

Linux mini-course

2011-02-18T18:17:00.004+01:00

Interest has been expressed in the Linux mini-course (read more about it here). Please contact the manager if you are interested in attending! Date and time are as yet not set.

Matlab learning activity

2011-02-18T18:15:00.002+01:00

The Matlab event on Tuesday 22nd of February is now full, but if interest is large enough we will give it again. Read more about it at

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

Welcome back Ariadna!

2011-02-18T18:11:00.003+01:00

SMILE is again visited by Ariadna Besga, who is a postdoc at Carlos III Health Institute, Madrid, Spain. Ariadna will stay until April 15th, and will give a talk on Thursday 7th of April.

Our guest from the Netherlands, Inge van der Kroon, will also present a talk, on Thursday 14th of April.