Freesurfer

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30088 discussions

open PhD position
by Esther Walton 14 Mar '12

14 Mar '12

Research position (PhD) in translational developmental neuroscience (with a focus on eating disorders) at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Dresden University of Technology, Germany PLEASE REPOST FOR INTERESTED PARTIES Job Description: The Department of Child and Adolescent Psychiatry, Dresden University of Technology, Germany invites applications for a research position (PhD) in neuroimaging of eating disorders (ED). We are interested in cognitive control, reward system and the processing of emotions in patients with anorexia nervosa. This is a full time position within the Translational Developmental Neuroscience Group. Responsibilities will include the coordination of our ongoing clinical study and the acquisition and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. Imaging sessions will take place on the Neuroimaging Center's 3T Siemens TIM-Trio scanner and data collected includes high-quality structural, diffusion, and functional MRI data. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, physiological and endocrinological information. The successful applicant will work in a team of young investigators and also be responsible to supervise interns and medical students working in the project. Applicants for the position must have completed (a) a Master or Diploma degree in a relevant field (Psychology, Neurosciences or Medicine; if you have additional qualifications a degree in Biology, Biomedicine, Biophysics, Computer Science or Electrical Engineering may also be sufficient), (b) have had some exposure to cognitive and emotional neurosciences, (c) participated in research activities within the past years (d) possess strong organizational skills and (e) be able to communicate in German with non-scientific staff members. Experience in computer programming (Linux/Unix shell scripting, Python and/or MATLAB), neuroimaging analysis methods (FSL, SPM, FreeSurfer), advanced statistical analyses is of advantage but not a precondition. The successful applicant will join a multidisciplinary team of researchers and clinicians and will receive further training in psychometric and endocrinological techniques and the application of analysis tools for neuroimaging data. Psychologists or physicians who wish to advance in their clinical training may be able to dedicate a small amount of their time to work with patients. The position is available for a start date as soon as April 15th 2012 (to be confirmed). Review of applications will begin immediately and will continue until the position is filled. The position is guaranteed for one year with the possibility of renewal after positive evaluation. Salary will be consistent with levels in accordance with the German Research Foundation (50% TV-L: E 13). Compensation includes health insurance, and vacation time. To apply you can use our online portal (http://www.uniklinikum-dresden.de/bildung-und-karriere/stellenangebote/wiss… application should include a cover letter detailing professional objectives and interests, CV (with grades), and the names and email addresses of two references. The application can be written in German or English. Applications from many disciplines may be considered. The position is open to qualified international applicants but the knowledge of some German is necessary since the position includes the coordination of an ongoing clinical study. Applicants with a disability will be given preference in the selection process. Prof. Dr. med. Stefan Ehrlich Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus Dresden an der TU Dresden E-Mail: KJPChefsekretariat(a)uniklinikum-dresden.de Please refer to our homepage: http://www.kjp-dresden.de/en/Eating-disorders, http://www.kjp-dresden.de/en/Schizophrenia and http://kjp-dresden.de/de/Publikationsliste-Prof-Dr-S-Ehrlich for more detailed information.

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wm.mgz "key"
by Michael Harms 13 Mar '12

13 Mar '12

Hello, Is there a "key" for what all the various altered voxel values in wm.mgz represent? For example, I know that if you manually add a voxel, it gets set to 255, and if you delete a voxel it gets set to 1. What is the analogous "key" for values of 200, 215, 230, and 250? thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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mri_vol2surf
by Tina Jeon 13 Mar '12

13 Mar '12

Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing "SetSlice $gnVolSlice [set gnVolSlice]" invoked from within ".w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc" (command bound to event) ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Re: [Freesurfer] White matter intensity normalisation
by Bruce Fischl 13 Mar '12

13 Mar '12

Hi Charlotte the aim of the WM intensity normalization is to center the white matter class mean around 110 and to "flatten" it over space, so that the mean is spatially stationary. It is certainly harder with 1.5T data that will be noisier than 3T (depending on the receive coil you use), but why do you say it didn't work very well? You need to visually inspect the surface accuracy to determine that. cheers Bruce On Tue, 13 Mar 2012, Charlotte Bernard wrote: > Thanks for your answer. But could you explain to me the aim of the white > matter intensity normalisation. What is the incidence if this step doesn't > work very well? > In my subjects, we can see that the quality of this process is not very > well! Maybe due to the acquisition on 1.5T?? > Thanks, > > > Date: Mon, 12 Mar 2012 08:50:02 -0400 > > From: fischl(a)nmr.mgh.harvard.edu > > To: chakeba(a)live.fr > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] White matter intensity normalisation > > > > Hi Charlotte > > > > have you visually inspected them? I would be more concerned about the # of > > voxels in wm which is way too low, but it looks like you eroded the wm > > mask, so maybe it's ok. Take a look at the surfaces over the data in > > tkmedit and see if it appears accurate in subjects like #8. The WM > > intensity won't be exactly 110, and is usually below it due to partial > > volume effects. > > > > cheers > > Bruce > > > > On Mon, 12 Mar 2012, Charlotte Bernard > > wrote: > > > > > Dear Freesurfer users, > > > > > > I run FS on my 670 subjects. All the scans were acquired on a 1.5T > Philips > > > scan. > > > I noticed that my values in the WM are near 100-110 but not exactly 110. > I > > > think it is a problem! Is it link to the 1.5T? How can I fix it? > > > I joined my log file of QA tools: could you help me to undertand the > output? > > > > > > wm-anat-snr results: > > > > > > SNR: Anatomical signal-to-noise ratio in white matter > > > mWM: Mean white matter intensity value > > > stdWM: Standard deviation of white matter intensity value > > > voxWM: Total number of white matter voxels in eroded mask > > > > > > SubjID SNR mWM stdWM voxWM > > > 1 13,37* 104,18 7,79* 24181 <------ > > > 2 14,79* 105,90 7,16* 22148 <------ > > > 3 13,57* 104,75 7,72* 37341 <------ > > > 4 12,67* 104,18 8,22* 29311 <------ > > > 5 14,36* 105,44 7,34* 48083 <------ > > > 6 11,40* 103,92 9,11* 47704 <------ > > > 7 14,52* 104,71 7,21* 25706 <------ > > > 8 9,92 101,42 10,22 40187 > > > 9 11,31* 104,28 9,22* 22967 <------ > > > 10 11,61* 102,92 8,86* 19850 <------ > > > 11 14,78* 105,05 7,11* 26607 <------ > > > 12 11,36* 105,33 9,27* 15465 <------ > > > 13 11,30* 103,69 9,18* 34685 <------ > > > 14 11,73* 105,20 8,97* 40471 <------ > > > 15 11,92* 104,04 8,73* 13777 <------ > > > 16 9,46 102,04 10,79 30314 > > > 17 12,60* 106,40 8,44* 38432 <------ > > > > > > I thought it can help me to quickly identify the subjects who didn't > work > > > for this step. For example, the subject n°8 has a problem? > > > > > > > > > Thanks, > > > Charlotte > > > > > > > > > > > > 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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recon and qdec error
by Michels Lars 13 Mar '12

13 Mar '12

Dear Freesurfer community I just installed Freesurfer 5.1 on our LINUX machine (Fedora 14) I then tried to construct volume and surface files (autorecon1 only) for the sample data set ('bert') and received the following error: /home/fsl/data/freesurfer/subjects/bert/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: tkregister2_cmdl failed, see transforms/talairach_avi.log Any ideas or suggestions? In addition, I wanted to start qdec and got the following message: qdec.bin: error while loading shared libraries: libvtkverdict.so.vtk5.2.0: cannot open shared object file: No such file or directory Again, any ideas? Thanks for your help Lars Dr. phil. L. Michels, Oberassistent Institute of Neuroradiology University Hospital of Zurich Frauenklinikstrasse 10 CH 8091, Switzerland FON +41-44-255-4965 Fax +41-44-255-8946

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Question regarding control points
by Martijn Steenwijk 12 Mar '12

12 Mar '12

Dear all, I've been correcting a recon with controlpoints and correction of the skull strip. Although the result is a lot better, still a part of the temporal lobe is missed, although I have been putting control points in this area. Is there a way to improve this? See attached image (left: pre-correction, right: post-correction). Best, Martijn

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[freesurfer] Is there any way to get the image from Tksurfer with white background?
by zhang mingxia 12 Mar '12

12 Mar '12

Hi dear freesurfer experts, I am making pictures for publication. The images saving from Tksurfer are black backgrounds. Is there any way to save the image with white background? Thank you very much Mingxia Zhang

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mri_glmfit -sim processing time?
by Juke Cha 12 Mar '12

12 Mar '12

Hi all, I'm running a simulation to get corrected p values. I set the iteration as 5000 times and it's a group analysis of ~40 subjects. Now the simulation has been going for three days on 2.8 Hz i7 CPUs and not done yet. Simulation on 100 iterations completed pretty quick so assumed a couple of days would be enough. Is this supposed to be this long? Is there any way to check if something goes wrong? Best, Juke -- Juke Cha, M.S. Ph.D Candidate, Program in Neuroscience Laboratory for Computational Neurodiagnostics (LCN)<http://www.lcneuro.org/> Dept of Biomedical Engineering Stony Brook University School of Medicine email: cha(a)lcneuro.org office: 631-632-1992 fax: 631-632-3222

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question about fcfast
by yingtan＠nmr.mgh.harvard.edu 12 Mar '12

12 Mar '12

Hello, everyone, I have question about fcfast. we have several bold numbers and run fcfast at the same time. For example, fcfast -id 070324_4TT00201 -mpr 3 -bold 15,16 -roi /ncf/tools/mtt24/seeds/N12Trio_avg152T1_reg6mm_40_-18_48.nii.gz I don't know if the final correlation (Z) images are mean value when fcfast completes the fcMRI anaysis. Thanks in advance. Best, Ying Tan

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dt_recon with siemens skyra data
by John Fredy 12 Mar '12

12 Mar '12

Hello all, I am trying to process siemen dti data from a skyra model in the dt_recon software. But the software fails in the conversion from Dicom. Anyone had experience with the DTI sequence from a skyra model? Any suggestion is welcome Thanks in advance John Ochoa Bioingeniería Universidad de Antioquia

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