Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Sulcal CSF Volume
by Mohammed Goryawala 23 Oct '14

23 Oct '14

Hello FreeSurfer Experts, Is it possible to estimate the sulcal CSF volume in Freesurfer processing? If not directly are there any indirect means that can give me an estimate? Thank you Mohammed Goryawala, PhD Department of Radiology Miller School of Medicine, University of Miami

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Re: [Freesurfer] longitudinal base template creation with one timepoint
by Martin Reuter 23 Oct '14

23 Oct '14

Hi Tracy, When you call recon-all -base simply pass only the single time point -tp. Best Martin Sent via my smartphone, please excuse brevity. <div>-------- Original message --------</div><div>From: Tracy Melzer <tracy.melzer(a)otago.ac.nz> </div><div>Date:10/22/2014 10:59 PM (GMT-05:00) </div><div>To: freesurfer(a)nmr.mgh.harvard.edu </div><div>Subject: [Freesurfer] longitudinal base template creation with one timepoint </div><div> </div>Dear FreeSurfer Experts, I am interested in how the longitudinal stream creates a base template with only a single image. Could someone please explain how or point me to a reference as to how this is accomplished? Thank you, Tracy Melzer

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Research Assistant Job: Northwestern Univ. Alzheimer's Disease Center (Chicago, IL)
by Emily Rogalski 23 Oct '14

23 Oct '14

Research Study Assistant job available at Northwestern University’s Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL. The research assistant will be responsible for analysis of neuroimaging datasets, in order to contribute to neuroscientific studies of normal aging and pathological aging. Duties include coordinating PET and MRI scans, and analyzing the resultant structural and functional imaging data. The RA will also have the opportunity to administer and score neuropsychological tests. Additional duties include working on graphics for manuscripts and grants or other general lab responsibilities. Candidates must have proficiency with computer programming, ideally with relevant technical languages such as MATLAB or Python. They must be willing to learn new MRI analysis software and troubleshoot problems independently. Prior experience with neuroimaging analysis suites such as Freesurfer, FSL, or SPM would be extremely useful. Relevant backgrounds would be in Neuroscience, Biology, Psychology, Computer Science, Mathematics, and Biomedical Engineering. *Minimum Qualifications: * - The candidate must hold a Bachelor degree. - Candidate must be fluent in at least one programming language. - A two-year commitment is requested. *Preferred Qualifications: * - Experience using Freesurfer or other neuroimaging platforms. Interested applicants can apply online here: http://www.northwestern.edu/hr/careers/ Job ID: 24257 If you have specific questions please email: e-rogalski(a)northwestern.edu To learn more about our center please go to: www.brain.northwestern.edu -- Emily J Rogalski, PhD Associate Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

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Bus error still when trying to launch tksurfer
by Claire Morley 23 Oct '14

23 Oct '14

Hello again Bruce, Thanks so much for your reply. I tried uninstalling XQuartz completely and reinstalling it, and I`m still getting the bus error. I have XQuartz`s newest version (2.7.7) that was launched in August of this year installed and it works with Macs 10.6 and newer. My Mac environment is such: Mac OS X Snow Leopard 10.6.8 Memory: 4GB 1067 MHz DDR3 Model Name: iMac Model Identifier: iMac10,1 Processor Name: Intel Core 2 Duo Processor Speed: 3.06 GHz Number Of Processors: 1 Total Number Of Cores: 2 L2 Cache: 3 MB Memory: 4 GB Bus Speed: 1.07 GHz Boot ROM Version: IM101.00CC.B00 Any further ideas what might be going on? Do I need a newer version of OS X in order to use Freesurfer optimally? Thank you so much again for your time! All the best, Claire On Mon, Oct 20, 2014 at 6:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. GLM contrast vector for continuous variable interaction > (Bronwyn Overs) > 2. Bus error when trying to launch tksurfer (Claire Morley) > 3. Re: Bus error when trying to launch tksurfer (J?rgen H?nggi) > 4. Re: Bus error when trying to launch tksurfer (Bruce Fischl) > 5. Do not have 'recon edit' button! Please help! (Smaragdi A.) > 6. Re: Do not have 'recon edit' button! Please help! (Bruce Fischl) > 7. Re: Do not have 'recon edit' button! Please help! (Smaragdi A.) > 8. unpacksdcmdir (Alshikho, Mohamad J.) > 9. Re: unpacksdcmdir (Shantanu Ghosh) > 10. Re: unpacksdcmdir (Douglas N Greve) > 11. Re: GLM contrast vector for continuous variable interaction > (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 20 Oct 2014 09:33:13 +1100 > From: Bronwyn Overs <b.overs(a)neura.edu.au> > Subject: [Freesurfer] GLM contrast vector for continuous variable > interaction > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <54443C29.9000309(a)neura.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Freesurfer Mailing List, > > I am running a GLM in freesurfer 2 categorical variables (2 levels), and > three continuous variables (age, prs, & sles). My fsgd file looks like > this: > > GroupDescriptorFile 1 > Title GLM_sles-group-gender-age > Class genderMale-groupControl > Class genderFemale-groupControl > Class genderMale-groupAtRisk > Class genderFemale-groupAtRisk > Variables age prs sles > Input ID_001 genderFemale-groupAtRisk 20 21 96 > Input ID_002 genderFemale-groupControl 21 13 79 > ... > > I want to test for an interaction between prs and sles, while > controlling for age, gender, and group. Can you tell me if the following > contrast vector will correctly test for this interaction: > > 0 0 0 0 0 0 0 0 0 0 0 0 0.5 > 0.5 0.5 0.5 > 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0 > 0 0 0 > > -- > > Kind regards, > > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 > > neura.edu.au <http://neura.edu.au> > > Follow @neuraustralia on twitter > <https://twitter.com/neuraustralia>Follow NeuRA on facebook > <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the > NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> > >

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Fwd: A BBVA Foundation-UPM Chair on Biomedical Imaging
by José Ángel Pineda 23 Oct '14

23 Oct '14

Notification of the “Isaac Peral” Program to contract one senior researcher associated with BBVA Foundation-UPM Industry-Academia chairs for scientific-technological research in Medical Imaging, within Marie Curie Action COFUND. This notice provides for a maximum of one position in the area of scientific-technological initiatives in Biotech indicated below, in accordance with the procedure established in the Regulatory Bases of 30 April 2009 for the ISAAC PERAL Program for Senior UPM Researchers (in the attached document). The candidate degree may be from any specialization in Engineering, Physics, Mathematics, Statistics, Biology, Biochemistry, etc. Location: The activities will be carried out in the Campus of International Excellence: Campus of Montegancedo at the CTB: Centre for Biomedical Technology (www.ctb.upm.es) in Madrid, Spain. Beneficiaries: 1. Have held a PhD for more than 10 years, effectively pursuing uninterrupted research activity during that time. 2. Have extensive research experience in the sphere of the profile of the contract announced, i.e. biomedical imaging. 3. Have pursued their research activity following the award of their PhD in relevant foreign Research Centers for at least six years or have studied the whole of the PhD and graduated in a foreign University or Research Centre and have pursued subsequent research activity in a relevant foreign research center for at least three years. 4. Have certified experience in the management of research groups in university institutions or relevant research centers. All the requirements demanded and the merits argued by candidates must have been fulfilled prior to the date of termination of the period for the submission of applications. N.B.: The details of the call will be published soon, although they will be very similar to those of the previous call (declared desert), that can be seen at: *http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servicio%20de%20Investigacion/Ayudas_y_Convocatorias/Convocatorias_Propias/Convocatoria-MedImaging-Eng.pdf <http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servici…>* Regulatory bases can be seen at: http://www.upm.es/internacional/Researchers/Post_DoctoralandResearchCareerP… Any questions, please feel free to contact the director of the CTB (Francisco del Pozo Guerrero - francisco.delpozo(a)ctb.upm.es) [image: http://www.upm.es/sfs/Montegancedo/Noticias/imagenes/ctb.gif] Prof. Francisco del Pozo Director Center for Biomedical Technology (CTB) Universidad Politécnica de Madrid Parque Científico y Tecnológico de la UPM Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, ES Tfo: +34 913364632 (Tfo: +34 913364631) www.ctb.upm.es -- José Angel Pineda Pardo Center of Biomedical Technology (CTB) Parque Científico y Tecnológico de la UPM Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, ES

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Postdoctoral Fellow in Analysis of Cross-Species fMRI and/or Neurophysiology
by Thomas Yeo 23 Oct '14

23 Oct '14

Dear All, I am looking to hire a postdoc to develop novel tools for fMRI and/or neurophysiology analysis. Details below. Cheers, Thomas Project: Develop computational tools for discovering (1) homologies and divergences between macaque and human brain organization using resting-fMRI and/or (2) relationship between macaque brain network organization revealed by fMRI versus neurophysiological recordings. Requirements: Ph.D. in computer science, electrical engineering, statistics, computational neuroscience or related fields. The successful applicant will work with an interdisciplinary team of computer scientists and neuroscientists, and must be willing to learn some neuroscience. Research Webpage: https://sites.google.com/site/yeoyeo02/home Compensation: Competitive and commensurate with experience Attraction: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Contact: Email BT Thomas Yeo (thomas.yeo(a)nus.edu.sg) with your CV. Deadline: Whenever the position is filled.

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Postdoctoral Fellow in Human-Macaque Brain Network Organization
by Thomas Yeo 23 Oct '14

23 Oct '14

Dear All, I am looking to hire a postdoc in human-macaque brain organization. Details below. Cheers, Thomas Project: (1) Discover homologies and divergences between macaque and human brain organization using resting-fMRI and/or (2) Elucidate relationship between macaque brain network organization revealed by fMRI versus neurophysiological recordings. Requirements: PhD in neuroscience, psychology, cognitive science or related fields. The successful applicant will work with an interdisciplinary team of computer scientists and neuroscientists, and must be willing to do some programming. Research Webpage: https://sites.google.com/site/yeoyeo02/home Compensation: Competitive and commensurate with experience Attraction: The National University of Singapore (NUS) boasts one of the few primate neurophysiology labs in the world. Perform ground-breaking research at NUS, while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Contact: Email BT Thomas Yeo (thomas.yeo(a)nus.edu.sg) with your CV. Deadline: Whenever the position is filled.

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longitudinal base template creation with one timepoint
by Tracy Melzer 23 Oct '14

23 Oct '14

Dear FreeSurfer Experts, I am interested in how the longitudinal stream creates a base template with only a single image. Could someone please explain how or point me to a reference as to how this is accomplished? Thank you, Tracy Melzer

2 1

freesurfer trouble with FTLD subjects
by Adam Mezher 22 Oct '14

22 Oct '14

Hi All, I'm running a number of subjects who have FTLD and their surfarce/parcellation outputs are quite poor (especially in the frontal lobe obviously). Are there any expert commands that can be used to attempt to fix this issue without having to do individual edits? Most of the subjects have underestimations in most frontal gyri and insula. Thanks a lot, Adam Adam Mezher USC Imaging Genetics Center Marina Del Rey, CA

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Creating an ROI mask for Cortical Thickness Analysis
by Smith, Michael 22 Oct '14

22 Oct '14

Hello Freesurfer’s I am trying to look at the cortical thickness for a specific ROI on the cortical surface (Primary Auditory Cortex: transverse temporal gyri). I found a specific tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) however the tutorial assumes I already have an ROI mask created. I was wondering if anyone had any tips on creating an ROI for the cortical surface from the parcellation/annotation files. I know you can “hand-draw” ROI’s in tkmedit or freeview but I would prefer something less subjective that doesn’t rely on my untrained eye and unsteady hand! Thanks in advance. Best, Michael S.

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