Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

sliver problem remains after going through relevant wiki page
by dahlia＠nmr.mgh.harvard.edu 05 Feb '10

05 Feb '10

Hi, I have just installed freesurfer on a CentoOS5 virtual machine (VMware), where the host OS is Windows. I am experiencing the "sliver problem" - only a sliver of the brain is being rendered to view. I have gone through the steps described in http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems, as follows: 1. NVidia driver update: the virtual machine doesn't have a /usr/bin/nvidia-installer, but I updated the driver installed on the host machine. Is this good enough, or should I update it somewhere under the virtual machine too? 2. doublebufferflag - I tried setting it to 1, but that didn't help 3. VirtualGL - since I'm sitting directly at the virtual machine, I didn't install this. 4. Override native graphics libraries: tried it too (copied the relevant file from the Martinos Center and set the LD_LIBRARY_PATH to its directory), no change. 5. VirtualBox - I didn't install this since the virtualization tool I'm using is VMware Workstation, not VirtualBox. Is there a way to run the relevant freesurfer version on a VMware virtual machine? I have done enough installation work on this machine that the option of using VirtualBox instead is strongly unappealing. Can anyone instruct me how to resolve this issue? Thanks!! Dahlia.

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2010 FSL & FreeSurfer course in Heidelberg, Germany
by Bruce Fischl 05 Feb '10

05 Feb '10

if you missed it the first time... > > We are pleased to announce the 2010 FSL & FreeSurfer course in > Heidelberg, Germany. It will run immediately before the Human Brain > Mapping conference, which will be in Barcelona - a 2-hour flight > from the Heidelberg area. The course is an official satellite > meeting of the HBM conference. > > The course lasts 5 days, from May 31 to June 4. > Numbers of attendees are strictly limited and are available on a > first-come-first-served basis. > > For full information and to register for the course, please go to: > > http://www.fmrib.ox.ac.uk/fslcourse/heidelberg2010.html > > Regards, course organisers. > > > > > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve(a)fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------

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use of Freesurfer in 2-4 year olds
by Naama Barnea-Goraly 05 Feb '10

05 Feb '10

Dear Freesurfer experts, We would like to use Freesurfer in a group of children 2-4 years of age. Is there a pediatric template in the works? How valid is it to use Freesurfer currently in this age group? Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you.

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multiple comparison correction using monte carlo
by Casper van Oers 05 Feb '10

05 Feb '10

Hi, I have performed a linear mixed model analysis on surface data in AFNI using SUMA, resulting in each vertex having a p value. I would like to perform a multiple comparison correction using freesurfer, as an FDR approach in AFNI is to stringent (individual vertex statistical thresholds are low). I would like to run a monte carlo simulation using mri_glmfit on a similar surface with similar parameters to extract a cluster threshold. I am not used to using freesurfer, so bear with me, please. 1) I have created a fsgd file defining the structure of the analysis used. This seems to be the tricky part, as I don't know how to exactly specify the model used. Maybe it suffices to define the data structure. There is two groups (patients, controls) and three timepoints. I want to correct for the group between group difference (contrast 1 -1), but don't know how to specify multiple timepoints per subject. 2) I have smoothed the data with fwhm 3mm in afni. How can I perform the simulation using mri_glmfit-sim and how can I do this without doing the analysis itself in freesurfer? I would appreciate your advice! Casper -- Casper A.M.M. van Oers, MD Department of Neurology, C03.236 University Medical Centre PO Box 85500 3508 GA Utrecht the Netherlands T: +31 30 2503184 F: +31 30 2542100 (Dept. of neurology)

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mri_diff geometry differences
by Michael Harms 04 Feb '10

04 Feb '10

Hello, What do "geometry differences" represent in the output of mri_diff? i.e., What do the numbers in the following output from mri_diff represent? Volumes differ in geometry 1 4 0.000015 Volumes differ in geometry 2 1 0.000000 thanks, -Mike H. -- 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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RES: Re: how to QC hippocampal measurement
by "Pedro Paulo de Magalhães Oliveira Junior" 04 Feb '10

04 Feb '10

In our AD paper (Journal of Alzheimer's disease) has some standard values for AD and non-demented -- @mobile -----Msg original----- De: Nick Schmansky Enviado: 04/02/2010 17:07:02 Para: Guang Zeng Cc: freesurfer(a)nmr.mgh.harvard.edu Assunto: Re: [Freesurfer] how to QC hippocampal measurement a simple way is to just plot the values. if a segmentation is horribly wrong, then its value will be way out of bounds compared to the others. note that there will be quite a bit of variation in size because of the AD subjects, so this method is just a simple QC. n. On Thu, 2010-02-04 at 12:58 -0600, Guang Zeng wrote: > Hi, there, > > I have used FreeSurfer to measure the hippocampal size of 200 ADNI > subjects, and now I'd like to QC the hippocampal measurement. > Anyone can give me some suggestion to do this, instead of loading they > one-by-one ? > > Thanks! > Guang > > > ______________________________________________________________________ > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up > now. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Research Assistant Position
by Victoria Williams 04 Feb '10

04 Feb '10

Two Research Assistant Positions in Neuroimaging of Traumatic Brain Injury and Post Traumatic Stress Disorder: Boston, MA, 02130, USA Employer: VA Boston Healthcare System Tags: Neuroimaging Neuropsychology/neuropsychological assessment/cognitive neuroscience Traumatic Brain Injury Post Traumatic Stress Disorder MRI, DTI, FMRI, ASL Programming Research assistant/RA PLEASE REPOST FOR INTERESTED PARTIES Job Description: The VA Boston Healthcare System and the VA Boston Neuroimaging Center invite applications for a research assistant position in neuroimaging of Traumatic Brain Injury (TBI) and Post Traumatic Stress Disorder (PTSD). This is a position within the newly funded VA Rehabilitation Research and Development Service TBI Center of Excellence Entitled "Translational Research Center for TBI and Stress Disorders (TRACTS)". Responsibilities will include acquisition and analysis of a range of magnetic resonance imaging (MRI) data collected for the TRACTS research program (including structural MRI, DTI, fMRI, and ASL). A second position will be focused more on technical infrastructural support for investigators involved with this project. TRACTS is a unique longitudinal study of over 300 Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) returning service members focused on understanding the neurological and cognitive consequences of blast exposure and differentiating the effects of blast from those of post traumatic stress. Experience in computer programming (Linux/Unix shell scripting and MATLAB), neuroimaging analysis methods (FSL, Freesurfer), and some statistical experience would be a plus. This position requires a minimum of a two year commitment (with opportunity for a longer position), and is available beginning immediately. Salary will be consistent with levels in accordance with the Boston VA Medical Center policies for research assistants. This is an optimal position for an individual who would like to obtain research experience before applying to graduate programs, or individuals that are looking for a more long-term position. Compensation includes full staff benefits, including health insurance, and vacation time. To apply or request more information, please send a CV and other relevant information to Dr. David Salat salat*at*nmr*dot*mgh*dot*harvard*dot*edu with the subject line "TRACTS RA position".

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Postdoctoral Position
by Victoria Williams 04 Feb '10

04 Feb '10

Postdoctoral Position in Neuroimaging of Traumatic Brain Injury and Post Traumatic Stress Disorder: Boston, MA, 02130, USA Employer: VA Boston Healthcare System Tags: Neuroimaging Neuropsychology/neuropsychological assessment/cognitive neuroscience Traumatic Brain Injury Post Traumatic Stress Disorder MRI, DTI, FMRI, ASL Programming Postdoctoral/postdoc PLEASE REPOST FOR INTERESTED PARTIES Job Description: The VA Boston Healthcare System and the VA Boston Neuroimaging Center invite applications for a postdoctoral research scholar position in neuroimaging of Traumatic Brain Injury (TBI) and Post Traumatic Stress Disorder (PTSD). This is a position within the newly funded VA Rehabilitation Research and Development Service TBI Center of Excellence Entitled "Translational Research Center for TBI and Stress Disorders (TRACTS)". Responsibilities will include analysis of a range of magnetic resonance imaging (MRI) data collected for the TRACTS research program (including structural MRI, DTI, fMRI, and ASL), as well as independent research that fits within the TRACTS framework. TRACTS is a unique longitudinal study of over 300 Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) returning service members focused on understanding the neurological and cognitive consequences of blast exposure and differentiating the effects of blast from those of post traumatic stress. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, medical history interviews, and a range of physiological information. 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. The successful applicant will join a multidisciplinary team of researchers examining a range of sequelae affecting returning service members. Experience in computer programming (Linux/Unix shell scripting and MATLAB), neuroimaging analysis methods (FSL, Freesurfer), and advanced statistical analyses would be a plus. This position requires a minimum of a two year commitment (with opportunity for a longer position), and is available beginning immediately. Salary will be consistent with levels in accordance with the Boston VA Medical Center policies for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. To apply or request more information, please send a CV and other relevant information to Dr. David Salat salat*at*nmr*dot*mgh*dot*harvard*dot*edu with the subject line "TRACTS Postdoctoral position".

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a question about mris_ca_train
by Guang Zeng 03 Feb '10

03 Feb '10

Hi, there, Recently, I sent sseveral emails to you to ask same kind of question about building our own template and atlas. Thanks a lot for your quick reply, they helps me a lot. Currently, I still have a question about building our own atlas using mris_ca_train, sorry to bother you again. We have a surface labeling atlas in our lab, we'd like to use this atlas instead of using FS's desikan_killiany.2007-06-20gcs. It is kind of difficult for us to load every subject in our training set to tksurfer, and manually label each ROI based on our ATLAS. What we try to do is: 1. Send each subject in the training set to our toolbox which will use our atlas to do surface labeling. For each subject it will output a file just like wmparc.mgz in FS, but it is NIfTI file. 2. Send each subject to FS pipeline to get the ?h.sphere.reg, ?h.sulc files. 3. Find a method to get my ?h. mylabels. annot files, and use mris_ca_train to build a new atlas. First of all, do you think what I try to do is reasonable? If yes, I know I need to get the FS .label files for each ROI, then I can call mris_label2annot to get ?h. mylabels. annot files. But how can I get the FS .label files for each ROI from our toolbox output ROI labeled NIfTI file? These qurstions trouble me for a long time, your help are really appreciate. Thanks a lot! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/

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where can I find write_annotation.m
by Guang Zeng 03 Feb '10

03 Feb '10

Hello, there, Where can I download write_annotation.m, I can not find it in my /matlab folder. Thanks! Guang _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/

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Freesurfer