[Freesurfer] Job offer: Neuroimaging scientist or clinician in Frankfurt
Dear all, I'm attaching a job offer for a fully-funded neuroimaging position at Frankfurt University, available immediately. The position is based at the Brain Imaging Center of Goethe University, a facility that hosts two dedicated research MR scanners and an MEG facility. A full clinical salary is available for applicants with a medical degree. Best, Johannes Dr Johannes C Klein Goethe-University of Frankfurt Department of Neurology, Brain Imaging Center Schleusenweg 2-16 D-60528 Frankfurt/Main Germany email: kl...@med.uni-frankfurt.de http://www.bic.uni-frankfurt.de/ The Department of Neurology and Brain Imaging Center (BIC) at the Goethe-University Frankfurt am Main invites applications for a full-time position as Clinician scientist (m/f) Or Doctoral/Postdoctoral researcher (m/f) We are seeking to recruit a highly motivated individual to develop a programme of research into imaging biomarkers of neurological diseases. Topics include the evolution of lesions in Multiple Sclerosis, the differentiation of neurodegenerative diseases, and the evaluation of target sites for deep brain stimulation (DBS) in movement disorders. Essential qualifications and interests include · a background in medicine, neuroscience, or a related field (e.g., a degree in psychology, engineering, physics, biology) · programming skills (Linux shell scripting, MATLAB) · an interest in biomedical questions and systems neuroscience · interpersonal skills when dealing with research subjects and colleagues Additionally, the ideal applicant · has experience with imaging software packages (e.g. FSL, SPM) · enjoys inter-disciplinary interactions with physicists and clinicians · has experience with conducting MRI scans · speaks (basic) German to interact with study subjects The successful candidate should have a demonstrated capacity for independent work and be capable of initiating research in a lively research environment. The post will involve collecting MRI data from patients with neurological conditions and normal volunteers. The post will also involve data analysis and writing of manuscripts for submission to peer-reviewed journals, as well as writing ethics applications for research projects. For Doctoral researchers, Goethe-University provides the opportunity to obtain a PhD degree. The Brain Imaging Center offers excellent imaging facilities, with two research-only 3T Siemens MRI scanners, MEG, various stimulus presentation methods, and an active physics group. The position is available immediately and can be split up. The appointment will be initially for 2 years, with the possibility of extension. Salary will be based on TV-Ä Hessen for Clinicians, and up to TVÖD-E13 for Postdoctoral Researchers. Goethe University is an equal opportunity employer. Applications from female candidates are encouraged. Where qualifications are equal, preference will be given to applicants with disabilities. Candidates should submit their applications (as a PDF including CV, names of at least two referees, and a brief letter of motivation outlining their interests and explaining how they meet the qualifications listed above) to Dr Johannes Klein (kl...@med.uni-frankfurt.de). Dr Klein is also available for informal enquiries. Applications will be considered until the post is filled. ___ 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] T1 mapping, mri_ms_fitparms and flip angle map
Dear all, For a structural study, I would like to determine cortical T1 values. T1 map generation from two FLASH images works like a charm, and I would like to add B1 correction now. I have acquired flip angle maps for my subjects (using the Yarnykh method with interleaved FLASH and two TRs), and would like to correct my T1 maps accordingly. Looking at the online help of mri_ms_fitparms, I think the parameter -afi should do the trick. However, I'm not sure about the properties of the flip angle map that I need to supply to mri_ms_fitparms. Does that programme expect absolute flip angle values? Or can I feed in my two AFI FLASH volumes in some way? If anyone can point me in the right direction, that would be great! Thanks for you help, Johannes ___ 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] T1 mapping, mri_ms_fitparms and flip angle map
Hi Bruce, Thanks a lot for your (very speedy) help! Cheers, Johannes Am 21 Nov 2011 um 18:21 schrieb Bruce Fischl: Hi Johannes you should give it a flip angle map in degrees. We assume that the nominal flip angle (that is, if B1 was homogeneous) would be 60 deg. cheers Bruce On Mon, 21 Nov 2011, Dr.med. Johannes C. Klein wrote: Dear all, For a structural study, I would like to determine cortical T1 values. T1 map generation from two FLASH images works like a charm, and I would like to add B1 correction now. I have acquired flip angle maps for my subjects (using the Yarnykh method with interleaved FLASH and two TRs), and would like to correct my T1 maps accordingly. Looking at the online help of mri_ms_fitparms, I think the parameter -afi should do the trick. However, I'm not sure about the properties of the flip angle map that I need to supply to mri_ms_fitparms. Does that programme expect absolute flip angle values? Or can I feed in my two AFI FLASH volumes in some way? If anyone can point me in the right direction, that would be great! Thanks for you help, Johannes ___ 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
Re: [Freesurfer] Best way to convert Philips par/rec to mgz
Dear Julie, The easiest way to preserve your data type would be to ask your Philips representative to switch DICOM export to 16 bit representation of the data. Alternatively, if you have access to an EasyVision console, you could try converting your .PAR/.REC into Analyze files with Philips' own tools. Otherwise, .PAR/.REC files deliver data in a flat format, so you could use the DICOMs to create a template volume in .mgh format, edit the datatype and attach the header to the .REC data (potentially swapping bytes and row ordering). This process is error prone though, and the .PAR/.REC-format is not well documented as far as I'm aware. Have you checked if your data actually use the 16 bits provided? Maybe you're not even losing anything. Cheers, Johannes Am 17.11.2009 um 20:53 schrieb Julie McEntee: Hello, I have T1-weighted data from Philips 3 T scanner obtained at a resolution of 0.898 X 0.898 X 0.9 mm in both dicom (8 bit) and par/rec (pixel size = int16) format. I would like to preserve the acquisition resolution of the data in par/rec format; what is the best way to convert such data to mgz format for analysis in freesurfer? A command line example would be helpful, as I am new to freesurfer. Thanks for your help, Julie Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] --out_orientation question using mri_convert
Dear all, I have acquired 4D data on a Siemens machine, and I'm using mri_convert to turn the DICOMs into NIFTI files. Now, I would like to rectify the 4D NIFTI volume, such that the principal axes display in a standard way in fslview. I can do this for 3D files like this is, and it works a charm for all sorts of original orientations: mri_convert --out_orientation LAS input.nii rectified_output.nii However, when I'm using a 4D NIFTi file as input, only the first volume is included in the rectified output and the rest is truncated. I was wondering if this is a known limitation, and if there is another tool I could use on 4D files which would save me having to split them up before reorientation? BTW, I've tried this on Freesurfer 4.3.0 and 4.0.5. Thanks in advance for your help, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
