Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

Two research positions (PhD) in translational developmental neuroscience at the TU Dresden
by Stefan Brauns 19 Aug '10

19 Aug '10

On behalf of Prof. Roessner/ PLEASE REPOST FOR INTERESTED PARTIES *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 *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). This is a full time position within the newly funded Translational Developmental Neuroscience Group. Some of the work will be carried out in close collaboration with scientists at the Charité - Universitätsmedizin Berlin and the Massachusetts General Hospital/ Harvard Medical School (Boston, USA). *Responsibilities* will include the acquisition and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, physiological and endocrinological 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. *Applicants for the position must have* completed (a) a Bachelor, Master or Diploma degree in a relevant field (Psychology, Biology, Biomedicine, Biophysics, Computer Science, Electrical Engineering) and (b) participated in research activities within the past years. Experience in computer programming (Linux/Unix shell scripting, C++ and/or MATLAB), neuroimaging analysis methods (FSL, SPM, FreeSurfer), advanced statistical analyses and scientific writing would be a plus. 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 some amount of their time to work with patients. *The position is available* for a start date as soon as September 15th 2010. 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* or request more information, please send a cover letter detailing professional objectives and interests, CV, and the names and email addresses of two references (all together in one pdf file in German or English) with the subject line “ED doctoral position" to the address below. Applications from many disciplines may be considered, and the position is open to *qualified international applicants*. Applicants with a disability will be given preference in the selection process. Prof. Dr. med. Veit Rößner Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus Dresden an der TU Dresden Goetheallee 12, 01309 Dresden E-Mail: KJPChefsekretariat(a)uniklinikum-dresden.de Please refer to our homepage: www.kjp-dresden.de for more detailed information.

1 0

CUDA installation error...
by Gonzalo Rojas Costa 19 Aug '10

19 Aug '10

Hi: I installed Freesurfer 5.0 and cudatoolkit_3.1_linux_32_ubuntu9.10 in Ubuntu 9.04... I tried to process a T1 volume with "recon-all -autorecon1 -s ingrid -use-gpu", but I got the error: "mri_em_register_cuda -skull nu.mgz /home/gonzalorojas/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : CUDA driver version is insufficient for CUDA runtime version. Linux image 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux recon-all -s ingrid exited with ERRORS at Thu Aug 19 10:05:03 CLT 2010" How can I solve the problem ?... Sincerely, Gonzalo Rojas Costa

2 3

Can -autorecon2-cp and -autorecon2-wm be run at the same time
by Paola Valsasina 19 Aug '10

19 Aug '10

Dear FreeSurfer experts, I am quite new to FreeSurfer and I am trying to analyze some patients. We run -autorecon2 step and we got some errors both in the intensitiy normalization and in the wm segmentation, so what we need to do now is both to add control points to the brainmask.mgz image and to slightly edit wm.mgz to fill holes. I am reading from the course slides the suggested workflow for running FreeSurfer, and it is suggested that 1) correction of intensitiy is performed (by adding control points and running of -autorecon2-cp) and 2) editing of wm is performed (by editing wm and running -autorecon2-wm). My question is: can I do both these steps together with a command line like: recon-all -s subject -autorecon2-cp -autorecon2-wm (after having done proper manual edits to both brainmask.mgz and wm.mgz) Or should I run only recon-all -s subject -autorecon2-cp, wait for the results of this step, check the wm output and proceed, if necessary, with -autorecon2-wm? I am asking this basically for saving time, but of course if it is not possible, we are proceeding with two separate steps Thank you for any advice Paola ------------------------------------------------------------- DAI IL TUO 5 X MILLE AL SAN RAFFAELE. BASTA UNA FIRMA. SE FIRMI PER LA RICERCA SANITARIA DEL SAN RAFFAELE DI MILANO, FIRMI PER TUTTI. C.F. 03 06 42 80 153 INFO: 5permille(a)hsr.it - www.5xmille.org

2 1

question about the -zgez flag with mri_convert
by Mehul Sampat 18 Aug '10

18 Aug '10

Hi Folks I use mri_convert to create nifti files from the dicom images from a 3T GE scanner. One of the option for mri_convert is "-zgez" with the following description from the mri_convert help: " -zgez, --zero_ge_z_offset set c_s=0 (appropriate for dicom files from GE machines with isocenter scanning)" Before the scan we "landmark" the subject; that is we set a point on the head coil to "0" and then proceed with the scan. Pardon the naive question, but does "isocenter scanning" refer to this step ? Also I created two nifti files with and without this flag; the only differences in the two headers were with in quartern_z field. without flag quartern_z = -50.061 and with the flag quartern_z = -90. (and one entry each in srow_z, sform, qform and vox2ras were also affected) Our scan has 180 slices and to me quartern_z = -90 seems the right one. is this correct ? Thanks Mehul

1 0

Fwd: [freesurfer] installation
by Ignacio Letelier 18 Aug '10

18 Aug '10

Sorry Doug I forgot to send the entire email thread. Now, could you please help me with the installation. Best regards. Forwarded conversation Subject: [freesurfer] installation ------------------------ From: *Ignacio Letelier* <nachoadress(a)gmail.com> Date: 2010/8/18 To: freesurfer(a)nmr.mgh.harvard.edu Hi all I'm a new freesurfer user and I have some troubles installing the program. after moving to cd /usr/local I typed *freesurfer-virtual:~>* tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz replacing <platform>-<release> with freesurfer-Linux-centos4-stable-pub-v4.3.1 I get the following error message Cannot >>* open: No such file or directory *>>* *>>* tar: Error is not recoverable: exiting now *>>* *>>* tar: Child returned status 2 *>>* *>>* tar: Error exit delayed from previous errors * I don´t know exactly what I'm doing wrong, this may happen because I'm not in the right directory or something? How can I get informnation about my Linux and Freesurfer software version.* * Any help will be greatly appreciated, thanks in advance -- Ignacio ---------- From: *Douglas N Greve* <greve(a)nmr.mgh.harvard.edu> Date: 2010/8/18 To: Ignacio Letelier <nachoadress(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Is that file in that directory? What size is it? Do you have write permissions to that folder? doug Ignacio Letelier wrote: > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ---------- From: *Ignacio Letelier* <nachoadress(a)gmail.com> Date: 2010/8/18 To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Hi Doug At least i've made sure that freesurfer location is in */usr/local/freesurfer * The Freesurfer properties tab says that it weights 3.1 GB Now, the Permissions tab says: *Owner*: freesurfer (freesurfer) *Access*: Read&Write *Group*: freesurfer *Acces*: Read only *Others* :Read only Thanks Doug -- Ignacio ---------- From: *Douglas N Greve* <greve(a)nmr.mgh.harvard.edu> Date: 2010/8/18 To: Ignacio Letelier <nachoadress(a)gmail.com> So do you have write access? Also, remember to send the entire email thread in the letter. I delete emails aggressively so I won't always know what you are talking about. Also, please respond to the list. Others may be interested, and it gets saved in the archive. doug ---------- From: *Ignacio Letelier* <nachoadress(a)gmail.com> Date: 2010/8/18 To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> 2010/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> I guess I do have write acces (according to with what I understood from my previous email) I'm not a Linux or Unix expert so help me please..... Thanks doug -- Ignacio ---------- From: *Douglas N Greve* <greve(a)nmr.mgh.harvard.edu> Date: 2010/8/18 To: Ignacio Letelier <nachoadress(a)gmail.com> Hi Ignacio, did you see the other requests in my email? doug Ignacio Letelier wrote: > > > 2010/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto: > greve(a)nmr.mgh.harvard.edu>> > -- Ignacio

2 1

User-defined colormaps
by Hansen, Kathleen (NIH/NIMH) [F] 18 Aug '10

18 Aug '10

Hello, If we are visualizing fmri surface data with tksurfer, how can we load our own user-defined colormaps? If this is not possible in tksurfer, is it possible using some other Freesurfer function? Thank you, Kathleen

2 1

installation of v5.0.0 without erasing v.4.5.0
by Gonzalo Rojas Costa 18 Aug '10

18 Aug '10

Hi: Can I install freesurfer v5.0.0 without erasing v.4.5.0 ?... Because I want to test some new features but I need to continue using v.4.5.0... I installed v.4.5.0 in /usr/local/freesurfer... Sincerely, Gonzalo Rojas Costa

2 1

[freesurfer] installation
by Ignacio Letelier 18 Aug '10

18 Aug '10

Hi all I'm a new freesurfer user and I have some troubles installing the program. after moving to cd /usr/local I typed *freesurfer-virtual:~>* tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz replacing <platform>-<release> with freesurfer-Linux-centos4-stable-pub-v4.3.1 I get the following error message Cannot >>* open: No such file or directory *>>* *>>* tar: Error is not recoverable: exiting now *>>* *>>* tar: Child returned status 2 *>>* *>>* tar: Error exit delayed from previous errors * I don´t know exactly what I'm doing wrong, this may happen because I'm not in the right directory or something? How can I get informnation about my Linux and Freesurfer software version.* * Any help will be greatly appreciated, thanks in advance -- Ignacio

2 1

using -nuintensitycor-3T flag with v-5.0.0
by Mehul Sampat 18 Aug '10

18 Aug '10

Hi Folks, I would like to use the -nuintensitycor-3T flag as listed in the release notes (http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) I had two questions about this new option: 1. Can I just use this as follows: recon-all -s bert -autorecon1 -autorecon2 -nuintensitycor-3T (then run -autorecon3) ? 2. I don't think there are any parameters associated with this flag. is this correct ? thanks Mehul

2 1

Curvature of the Corpus Callosum
by Alan Francis 17 Aug '10

17 Aug '10

Hi All: Does a lower score on the curvature index of the CC (as done by FreeSurfer) imply that the Corpus Callosum is more curved (smaller radius) or is it the other way around? thank you, Alan |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan Francis Brain Spectroscopy and Neuroimaging Lab Beth Israel Deaconess Medical Center Dept of Psychiatry Harvard Medical School Boston 02215

3 4

← Newer
1
...
4
5
6
7
8
9
10
...
16
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2010