Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Volume to surface dimension mismatch
by Lena Palaniyappan 20 Aug '10

20 Aug '10

I have a mask file which I need to overlay on the individual images of a group of subjects to extract thickness values within ht mask. But the mask is of dimension 2X2X2, will this be an issue? Thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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FreeSurferAlpha Label Volumes
by Mona 20 Aug '10

20 Aug '10

Hello, I'd like to extract hippocampal and PHC volumes from files reconstructed with FreeSurferAlpha. Is there a command for this or would you recommend re-reconstructing to obtain label volumes? Thank you, Mona

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Automatic Plotting of Hemodynamic Response???
by Adam Nitenson 20 Aug '10

20 Aug '10

Hello Freesurfers, I am currently running ROI analyses (dACC) and want to plot the timecourse of hemodynamic responses to a cognitive task (2 conditions) in a group of subjects. I have been using func2roi commands such as func2roi-sess -roidef lh_dACC -analysis RM_correct_error -anatlabel lh.dACC -maskcontrast error_vs_correct -maskthresh 0.000000001 -masktail pos -maskframe 5 -maskmap sig -sf /autofs/space/ventzl_036/users/RespMon12C/subject_lists/caitlin_SZerrorcorrect.txt -d /autofs/space/ventzl_036/users/RespMon12C/subjects and then roisummary to generate charts from which I create a hemodynamic curve through data manipulation. I was recently informed that there should be a way through which I could automatically plot such a hemodynamic curve, and that this method might not require a designated threshold as func2roi does (as we want any activation in the ROI to be considered). Is there any way to create a more automatic, streamlined hemodynamic response curve, or are func2roi and roisummary the standard means of doing this? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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mirror hemispheres
by johanna feiler 20 Aug '10

20 Aug '10

Hello FreeSurfers, I wonder if it is possible to mirror my complete data, so that the right hemisphere will be the left one and the other way round. I was thinking about using this command: fslswapdim <input> z -x -y <output and start with all the preprocessing steps afterwards. I want to use it for anatomical data only, so the question is if it will work with Freesurfer (not FSL) as well? Do you think it would work this way anyway? Or has anybody any other experiences with mirroring data? Any help will be appreciated! Best regards, Johanna Feiler ___________________________________________________________ Neu: WEB.DE De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: https://produkte.web.de/go/demail02

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whoops
by Adam Nitenson 19 Aug '10

19 Aug '10

Sorry for the double post (and, I suppose, the triple post as well) Only consider the more recent email, and it's just a completed version of my first one. Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Automatic Plotting of Hemodynamic Response???
by Adam Nitenson 19 Aug '10

19 Aug '10

Hello Freesurfers, I am currently using func2roi to analyze the hemodynamic response to a cognitive task within the dACC in a group of subjects. I have been constraining my analyses to 6 seconds post stimulus onset, a specific contrast (error_vs_correct), and with a very low threshold so that any activation in the area will be considered. Here is an example of a command that I have been using. func2roi-sess -roidef lh_dACC -analysis RM_correct_error -anatlabel lh.dACC -maskcontrast error_vs_correct -maskthresh 0.000000001 -masktail pos -maskframe 5 -maskmap sig -sf /autofs/space/ventzl_036/users/RespMon12C/subject_lists/caitlin_SZerrorcorrect.txt -d /autofs/space/ventzl_036/users/RespMon12C/subjects I then use roisummary-sess to generate charts of the results, and futher data organization allows me to plot the hemodynamic response curve. However, I was recently told that there should be a way to automatically generate such curves; a method that also does not require a maskthresh as func2roi does (as we essentially do not want any threshold). Are there any techniques, Freesurfer or otherwise, that might allow me to conduct such analyses in a more streamlined fashion, or is func2roi the standby command for such tasks? Thanks! Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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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.

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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

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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

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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

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