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.semailto: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.semailto:ivanka.savic-berglund@ki.se

On Dec 15, 2013, at 9:00 AM, <freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu> <freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:

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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)

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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

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

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

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

_______________________________________________ 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 *******************************************