[Freesurfer] open PhD position
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/wissenschaft/wissenschaftlicher-mitarbeiter-doktorand).The 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: kjpchefsekretar...@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. ___ 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 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.
[Freesurfer] open Research position (PhD)
___ 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 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.
[Freesurfer] open Post-doc position
Post-doc position within the Collaborative Research Centre 940 "Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions" at the Department of Child and Adolescent Psychiatry, University Hospital C. G. 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 postdoctoral research position in neuroimaging of eating disorders. The new project is part of the aforementioned Collaborative Research Centre (CRC, Steering Committee: Profs. T. Goschke, C. Kirschbaum, M. Smolka, A. Strobel, H.-U. Wittchen and will focus on 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 research study and the acquisition and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. Together with a doctoral student new functional MRI paradigms need to be implemented. 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 markers. Summarizing results and writing research articles will be another central aspect of the work. The successful applicant will work in a team of young investigators and also be responsible to supervise doctoral students, interns and medical students working in the project. Thanks to the CRC the applicant will have ample opportunity to work with peers and senior scientists in similar project in the Medical School and the Psychology Department. Applicants for the position must hold (a) a PhD, MD or comparable 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) published in peer-reviewed journals, e) possess strong organizational skills and (f) be able to communicate in German with non-scientific staff members. Some experience in computer programming (Linux/Unix shell scripting, Python and/or MATLAB), neuroimaging analysis methods (FSL, SPM, FreeSurfer or others), advanced statistical analyses and scientific publishing is necessary. The successful applicant will join a multidisciplinary team of researchers and clinicians, will receive further training and train doctoral students (informally). The position is available for a start date as soon as July 1st 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. The CRC funding has been granted for 4 years. Salary will be consistent with levels in accordance with the German Research Foundation (100% TV-L: E 13). Compensation includes health insurance, and vacation time. To apply you can use our online portal (https://www.uniklinikum-dresden.de/Bewerbung/?id=81ed34303f2d9930fe6a6cb5d3e641c4).The application should include a cover letter detailing professional objectives and interests, CV (with grades and language skills), 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: kjpchefsekretar...@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. ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please c
[Freesurfer] aparc+aseg2diff.mgz files
Hi, in $SUBJECTS_DIR/any_subject_ID/mri/ there are aparc+aseg2diff.mgz files and norm2diff.mgz files. What does the -2diff- mean and where does it come from? I suspect it's the reason why we have problems with one subject that has a 90 degree turn in fslview, since it was the only one, which didn't have -2diff- files thanks, Esther _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_2___ 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 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.
[Freesurfer] fixing cortical parcellation
Hi, I just came across a cortical parcellation issues (see attachment), which I got when running tksurfer M02111314 rh pial -annot aparc There is a small-ish orange blob (belonging to the parstriangularis) seeming to be misplaced slightly to the left onto the parsopercularis and I was wondering what ways there are to fix it. I look up the freesurfer wiki, but couldn't really find anything about this. I mean this wouldn't work with control points or the like, right? Thanks for your help, Esther _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2<>___ 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 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.
[Freesurfer] fsaverage label into MNI mask
Hi, I want to turn a fsaverage-label (lh.DLPFC.label) into a mask (nifti) in MNI space and used these two commands: 1) To turn the label into a volume (within $SUBJECTS_DIR): mri_label2vol --label lh.DLPFC.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o left_DLPFC_july19b.nii.gz --identity 2) To turn the DLPFC nifti into MNI space: mri_vol2vol --mov left_DLPFC_july19b.nii.gz --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o left_DLPFC_MNI_july19b.nii.gz --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat However, even though the final output file is in MNI, the ROI doesn't align with the MNI152 brain. Could it be that the FSL and the FS MNI152 brain are not the same and therefore the registration file is not the right one to use? Thanks for your help, Esther _ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5___ 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 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.
Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label
Thanks so much for your input. Could somebody please answer the second part of the question? That is, ignoring the fact that the label looks a bit weird as it is, is the overlay between the label and the volume okay, as seen in the second file I attached in my first email? If not, any idea what could have gone wrong? Thanks for all your help, Esther Date: Tue, 31 May 2011 10:36:06 +0200 From: christophe.destri...@univ-tours.fr To: estherkil...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label Hi Esther I had a look to the 2005 aparc for fsaverage and the intraparietal sulcus is indeed weird. Why don't you use the 2009 version of the atlas that includes major improvements ; this parcellation is fully described in Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. ; Destrieux C, Fischl B, Dale A, Halgren E. ; Neuroimage. 2010 Oct 15;53(1):1-15 I let Bruce or Doug answer the second part of your question ; cheers PS I attached a snapshot of the 2009 parcellation for the same hemi -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 De: "Esther Walton" À: freesurfer@nmr.mgh.harvard.edu Envoyé: Lundi 30 Mai 2011 23:41:24 Objet: [Freesurfer] S_intraparietal-and_Parietal_transverse.label Dear list, I am interested in the S_intraparietal-and_Parietal_transverse label from the Desitreux atlas using aparc.a2005s.annot. If I load this into fsaverage, it has three regions to it (see dark purple label in the attached screenshot): two big ones, very close to each other, connected by two narrow bridges, and another much smaller region more dorsally. Does this look fine to you?! Secondly, assuming this is ok, I created labels for each subject using mri_annotation2label and turned those labels into ROIs in standard space using mri_label2vol --label xx/label/lh.S_intraparietal-and_Parietal_transverse.label --temp xx/reg_standard/example_func.nii.gz --reg xx/reg/freesurfer/anat2std.register.dat --o xx/reg_standard/stats/lh.S_intraparietal-and_Parietal_transverse.nii.gz However, when I load this volume with: tksurfer fsaverage lh inflated -overlay lh.S_intraparietal-and_Parietal_transverse.nii.gz -mni152reg -fthresh 0.1 -fmax 1 it looks a bit off (see yellow label and red ROI in second screenshot). Would you think that's still ok taking into account the individual anatomy or did something go wrong somewhere? Thanks for your help, Esther ___ 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 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. ___ 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 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.___ 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 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.
Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label
Hi Bruce, Yes, I mean the one on the inflated surface. I found this view easier to judge how well the label and the nii.gz match. Is that a problem? Thanks, Esther > Date: Thu, 2 Jun 2011 08:36:27 -0400 > From: fis...@nmr.mgh.harvard.edu > To: estherkil...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label > > Hi Esther > > I don't see a volume overlay, just one on the inflated surface. Is that > what you mean? If not, can you resend and explain? > > Bruce > > On Thu, 2 Jun 2011, Esther Walton wrote: > > > > > Thanks so much for your input. > > > > Could somebody please answer the second part of the question? > > That is, ignoring the fact that the label looks a bit weird as it is, is > > the overlay between the label and the volume okay, as seen in the second > > file I attached in my first email? If not, any idea what could have gone > > wrong? > > > > Thanks for all your help, > > > > Esther > > > > Date: Tue, 31 May 2011 10:36:06 +0200 > > From: christophe.destri...@univ-tours.fr > > To: estherkil...@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label > > > > > > > > Hi Esther > > > > I had a look to the 2005 aparc for fsaverage and the intraparietal sulcus > > is indeed weird. > > > > Why don't you use the 2009 version of the atlas that includes major > > improvements ; this parcellation is fully described in > > > > Automatic parcellation of human cortical gyri and sulci using standard > > anatomical nomenclature. ; Destrieux C, Fischl B, Dale A, Halgren E. ; > > Neuroimage. 2010 Oct 15;53(1):1-15 > > > > I let Bruce or Doug answer the second part of your question ; cheers > > > > PS I attached a snapshot of the 2009 parcellation for the same hemi > > > > > ___ > 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 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. > ___ 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 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.
