Research Engineer position in Neuroscience

Karolinska Institutet, Dept for Women’s and Children’s Health

We are seeking a highly talented, innovative and enthusiastic researcher preferably with a PhD in physics and with experience of brain imaging (the latter is mandatory).

The research will be conducted at Div of Behavioral Neurology at the Department of Neurology Karolinska Hospital and Dept of Womens and Childrens Health, Karolinska Institute, which is part of the Stockholm Brain Institute (SBI). Our team consists of physicians, physicists, psychologists and biomedical experts, and our laboratory has expertise in functional magnetic resonance imaging (fMRI), PET, and psychophysics. In addition, the Stockholm Brain Institute has MeG and TMS facilities. We have access to two state-of-the-art 3-Tesla MRI scanners and the latest generation of the PET scanner at Karolinska Institute and Hospital.

 

The ideal candidate will have expertise in human brain imaging (PET, MRI), and mathematics, have knowledge about brain anatomy, and insight in experimental psychology. The applicant should have experience in MRI acquisition and analysis, excellent programming skills (eg Linux, Matlab, Python), basic knowledge of statistics and an appreciation of methodological issues in cognitive brain imaging. You will be thorough, efficient, a good communicator, and enjoy working as part of a diverse and energetic, interdisciplinary team. You will organize methodology workshops för PhD post doctoral students of the institution. You will also have many opportunities to own development including national and international workshops and meetings.

 

The candidate is expected to work within the general framework of the research program and actively contribute teaching and improve the MR methodology, with respect to data post processing. It is important that the candidate can independently keep updated to the latest software and their advantages. Applicants should be able to demonstrate a consistently good academic record, including publications in international journals. Applicants are expected to have the knowledge of post processing of the MRI data including analysis of fMRI time series with calculations of functional connectivity, multivariate pattern analysis, analyses of structural connectivity and computational morphometry, and gene brain interaction. There are several on going research programs covering various fields (e.g., effect of chronic stress on the brain, impact of sex hormones and sex chromosome genes on cerebral physiology and behaviour, the underpinnings of human epilepsy)

The position is for an initial 12-month period, with the possibility of a permanent contract. Applicants with a foreign PhD are welcome.


Application process


An application must contain the following documents in English:

  1. Curriculum vitae and qualifications, presented in accordance with Karolinska Institutet’s qualifications portfolio (http://ki.se/meritportfolj )
  2. A complete list of publications
  3. A summary of current work (no more than one page)
  4. Verifications for crediting of illness, military service, work for labour unions or student organizations, parental leave or similar circumstances
  5. Verification from the thesis defense committee or the equivalent (only if the thesis defense is scheduled within three months after the application deadline)

The application is to be submitted on the NetRecruiter system.

Application deadline: January 30, 2014

Start time is negotiable.

For additional information, please contact Professor Ivanka Savic, E-mail: ivanka.savic-berglund@ki.se

 

Ivanka Savic M.D., PhD
Professor of Neurology
Karolinska Institute
Dept of Women’s and Children’s Health and Neurology
Clinic,Karolinska Hospital, Q2:07
SE-171 76  STOCKHOLM, Sweden

Telephone +46 8 517 773 41
  +46 709 38 07 38 
Fax            +46 8 517 76 422
ivanka.savic-berglund@ki.se


On Dec 15, 2013, at 9:00 AM, <freesurfer-request@nmr.mgh.harvard.edu>
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Today's Topics:

  1. Re: Dura/pial reconstruction: FLAIR vs. multiecho (Bruce Fischl)
  2. Re: Fwd: Re: Fwd: Re: Fwd: Some problems of the brain image
     after recon-all (Bruce Fischl)
  3. Re: A prblem of tksufer tool (Bruce Fischl)
  4. Re: Dura/pial reconstruction: FLAIR vs. multiecho
     (Watson, Christopher)


----------------------------------------------------------------------

Message: 1
Date: Sat, 14 Dec 2013 13:09:20 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs.
multiecho
To: roberto.viviani@uni-ulm.de
Cc: Andre van der Kouwe <andre@nmr.mgh.harvard.edu>,
Freesurfer@nmr.mgh.harvard.edu, Eberhard.Pracht@dzne.de
Message-ID: <alpine.LRH.2.03.1312141308350.17965@nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Roberto

I think a T2-space FLAIR is your best bet. We have very little experience
with other FLAIR and/or/ T2s, but those seem to work well. They are *much*
higher SNR than the T2* maps that one can get from an memprage where the
last echo is only around 7ms.

cheers
Bruce
 On Sat, 14 Dec 2013,
roberto.viviani@uni-ulm.de wrote:

Dear all,

starting from the version of March of this year, FreeSurfer supports
the use of co-acquired FLAIR images to separate the dura from the gray
matter. Some years ago, the idea about solving the same problem was to
use multi-echo MPRAGE images. I am starting a new project, in which I
am planning to acquire structural images, and I would like to know
something more about these two ways of addressing the dura problem.

-- is there any experience on the superiority of the FLAIR approach,
or is there any published evaluation of it / comparison with the
MEMPRAGE approach (such as the van der Kouwer et al. 2008 paper on the
MEMPRAGE)  (I looked for it in scholar.google but could not find it)

-- are you planning to support the multi echo approach in the future,
or is it going to be discontinued

I will also be very interested to hear from anyone who has had any
experience with the FLAIR approach, or both.

Best wishes,
Roberto

Roberto Viviani
University of Ulm, Germany



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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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------------------------------

Message: 2
Date: Sat, 14 Dec 2013 13:15:55 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: Re: Fwd: Re: Fwd: Some problems of the
brain image after recon-all
To: "Xiaojun.Huang" <lvdosha@gmail.com>
Cc: Freesurfer@nmr.mgh.harvard.edu
Message-ID: <alpine.LRH.2.03.1312141315450.17965@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

sorry, I don't think I got it. How did you send it?
On Fri, 13 Dec 2013,
Xiaojun.Huang wrote:

Hi Bruce,
I Have sent the raw data to you and I find if it is the problem of tksurfer
Installing? Can it result in the problem? How can I Fix it?

Thanks,
Xiaojun.



-------- ???? --------
??:
Re: [Freesurfer] Fwd: Re: Fwd: Some problems of the brain image after
recon-all
??:
Tue, 10 Dec 2013 08:22:36 -0500 (EST)
???:
Bruce Fischl <fischl@nmr.mgh.harvard.edu>
???:
Xiaojun.Huang <lvdosha@gmail.com>

yes, or the whole subject dir so I can diagnose what went wrong

cheers
Bruce
On Tue, 10
Dec 2013, Xiaojun.Huang wrote:

Hi Bruce,
I wonder if  I need to upload the 3d raw data to you, If you need them.
Best,
Huang.
? 2013/12/7 0:12, Bruce Fischl ??:
it comes up upside down in tksurfer without pressing any buttons or
anything? Never seen that before - if you upload the subject I'll take a
look

cheers
Bruce
On Fri, 6 Dec 2013, Xiaojun.Huang wrote:

hi all,

I am processing the 3D PD patients brain now . After recon-all running,
the segmentations of the GM and WM is not accurate although the original

dat
a is normal. additionally, when I use the TKSurfer Tools to review the 3
D
brain,it is rev
erse.
More informations and images as follows:

-------- ???? --------
??:
Re: [Freesurfer] Fwd: Some problems of the brain image after recon-all
??:
Thu, 05 Dec 2013 12:45:10 +0800
???:
Xiaojun.Huang <lvdosha@gmail.com>
???:
Bruce Fischl <fischl@nmr.mgh.harvard.edu>

Hi Bruce,
Sorry for reply late.
The data were provided by a hospital and the input data were 3D
images.Some image informations as followed(eg.PDSub_02):

0008,103E,Series Description=Ax 3D VBM
0008,1090,Manufacturer's Model Name=SIGNA EXCITE
0018,0000,Acquisition Group Length=484
0018,0020,Scanning Sequence=GR
0018,0021,Sequence Variant=SS\SP\SK
0018,0022,Scan Options=FAST.GEMS\EDR.GEMS\FILTERED.GEMS
0018,0023,MR Acquisition Type=3D
0018,0025,Angio Flag=N
0018,0050,Slice Thickness=1
0018,0080,Repetition Time [TR, ms]=7.652
0018,0081,Echo Time [TE, ms]=3.312
0018,0082,Inversion Time=0
0018,0083,Number of Averages=1
0018,0084,Imaging Frequency=127.755675
0018,0085,Imaged Nucleus=1H
0018,0086,Echo Number=
0018,0087,Magnetic Field Strength=3
0018,0088,Spacing Between Slices=1
0018,0091,Echo Train Length=1
0018,0093,Percent Sampling=100
0018,0094,Percent Phase Field View=100
0018,0095,Pixel Bandwidth=97.6562
0018,1020,Software Version=12\LX\MR Software release.12.0.M5A.0819.a
0018,1030,Protocol Name=PDD-YANGWANQUN/4
0018,1310,Acquisition Matrix=0, 256, 228, 0
0018,1312,Phase Encoding Direction=ROW
0018,1314,Flip Angle=13
0018,1315,Variable Flip Angle Flag=N
0028,0010,Rows=512
0028,0011,Columns=512

It comes up in the proper orientation in tkmedit in three orientations a
s
attachment(eg.coromaland saggital view).

Tanks,
Xiaojun.


? 2013/12/4 22:45, Bruce Fischl ??:
Hi Xiaojun

we need more details in order to help you. What was your input data? >

What format was it in? Does it come up in the proper orientation in >
tkmedit? What kind of acquisition (resolution, type, etc...) did you use
?

cheers
Bruce
On Wed, 4 Dec 2013, Xiaojun.Huang wrote:




-------- ???? --------
??:
Some problems of the brain image after recon-all
??:
Tue, 03 Dec 2013 21:33:41 +0800
???:
Xiaojun.Huang <lvdosha@gmail.com>
???:
Freesurfer@nmr.mgh.harvard.edu


Hi,

I am processing the 3D PD patients brain now . After recon-all >>
running, the segmentations of the GM and WM is not accurate
although the original data is normal. additionally, when I use the >>

TKSurfer Tools to review the 3D brain,it is reverse. (eg.
PDSub_02 in the attach files)

It is the first time for me to use Freesurfer.I'm sorry for the >>
trouble I'm giving you.And looking forward your reply.

Thanks,
Xiaojun

2013.12.3







The information in this e-mail is intended only for the person to whom

it is
addressed. If you believe this e-mail was sent to you in error and the

e-mail
contains patient information, please contact the Partners Compliance >

HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you

in error
but does not contain patient information, please contact the sender >
and properly
dispose of the e-mail.














------------------------------

Message: 3
Date: Sat, 14 Dec 2013 13:17:24 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] A prblem of tksufer tool
To: Rujing Zha <charujing123@163.com>
Cc: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>, "Xiaojun.Huang"
<lvdosha@gmail.com>, freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1312141316240.17965@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Rujing

can you describe your freeview problems again?

thanks
Bruce


On Sat, 14 Dec 2013, Rujing Zha wrote:

Hi Huang,
I have similar question with you. In my case, I cannot visualizing inflated
image by tksurfer but freeview. Looking forward to someone's help.
All the best.
?
2013-12-14

____________________________________________________________________________
Rujing Zha

____________________________________________________________________________
????"Xiaojun.Huang" <lvdosha@gmail.com>
?????2013-12-14?20:44
???[Freesurfer] A prblem of tksufer tool
????"Freesurfer"<Freesurfer@nmr.mgh.harvard.edu>
???
?
Hi,?
I?am?processing?the?3D?PD?patients?brain?now?.?After?recon-all?running,?
when?I?use?the?TKSurfer?Tool?to?review?the?3D?brain,?it?is?reverse?and?
mistake?the?left?and?right.?I?test?some?other?data?and?realized?it?may?
be?something?wrong?with?the?Tksufer?installing.How?can?I?fix?it??
Thanks,?
Huang.?
_______________________________________________?
Freesurfer?mailing?list?
Freesurfer@nmr.mgh.harvard.edu?
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer?
?
?
The?information?in?this?e-mail?is?intended?only?for?the?person?to?whom?it?i
s?
addressed.?If?you?believe?this?e-mail?was?sent?to?you?in?error?and?the?e-ma
il?
contains?patient?information,?please?contact?the?Partners?Compliance?HelpLi
ne?at?
http://www.partners.org/complianceline?.?If?the?e-mail?was?sent?to?you?in?e
rror?
but?does?not?contain?patient?information,?please?contact?the?sender?and?pro
perly?
dispose?of?the?e-mail.?
?



------------------------------

Message: 4
Date: Sat, 14 Dec 2013 18:33:32 +0000
From: "Watson, Christopher" <Christopher.Watson@childrens.harvard.edu>
Subject: Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs.
multiecho
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>,
"roberto.viviani@uni-ulm.de" <roberto.viviani@uni-ulm.de>
Cc: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>,
Andre van der Kouwe <andre@nmr.mgh.harvard.edu>,
"Eberhard.Pracht@dzne.de" <Eberhard.Pracht@dzne.de>
Message-ID:
<C598595A8153064A89C29B0A55A55949487A4349@CHEXMBX2A.CHBOSTON.ORG>
Content-Type: text/plain; charset="us-ascii"

I only have anecdotal evidence based on 4 subjects, but I found that using the FLAIR results in much better surface reconstruction than the multiecho. In my experience (with kids age 12-16), the pial surface was underestimated when I used the multiecho.

________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu]
Sent: Saturday, December 14, 2013 1:10 PM
To: roberto.viviani@uni-ulm.de
Cc: Andre van der Kouwe; Freesurfer@nmr.mgh.harvard.edu; Eberhard.Pracht@dzne.de
Subject: Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs. multiecho

Hi Roberto

I think a T2-space FLAIR is your best bet. We have very little experience
with other FLAIR and/or/ T2s, but those seem to work well. They are *much*
higher SNR than the T2* maps that one can get from an memprage where the
last echo is only around 7ms.

cheers
Bruce
 On Sat, 14 Dec 2013,
roberto.viviani@uni-ulm.de wrote:

Dear all,

starting from the version of March of this year, FreeSurfer supports
the use of co-acquired FLAIR images to separate the dura from the gray
matter. Some years ago, the idea about solving the same problem was to
use multi-echo MPRAGE images. I am starting a new project, in which I
am planning to acquire structural images, and I would like to know
something more about these two ways of addressing the dura problem.

-- is there any experience on the superiority of the FLAIR approach,
or is there any published evaluation of it / comparison with the
MEMPRAGE approach (such as the van der Kouwer et al. 2008 paper on the
MEMPRAGE)  (I looked for it in scholar.google but could not find it)

-- are you planning to support the multi echo approach in the future,
or is it going to be discontinued

I will also be very interested to hear from anyone who has had any
experience with the FLAIR approach, or both.

Best wishes,
Roberto

Roberto Viviani
University of Ulm, Germany



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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




------------------------------

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End of Freesurfer Digest, Vol 118, Issue 28
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