Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

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3d slicer view only the post-central gyros
by asaf achiron 14 Apr '10

14 Apr '10

hello, How can i use 3d slicer to only view the post-central gyros without the other areas, than you Asaf

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Problem with tkmedit Edit Voxels Tool on Intel Mac
by Ed Gronenschild 14 Apr '10

14 Apr '10

Hi, On an Intel Mac the Edit Voxels Tool does not work, contrary to a PPC Mac. This applies both to version v4.3.1 and v4.5.0. Ed

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PROBLEMS WITH SEGMENTATION
by chesi.leonardo＠alice.it 14 Apr '10

14 Apr '10

Hi, I'm Leonardo an italian student of Pisa. I'm writing to you to ask if there's any way to correct this problem: we have a 3.0T machine with a 8 channels head coil to acquire the volumetric image. we have found a big inhomogeneity in the contrast of the image particularly in the frontal lobe where, so we think, the head is influenced by a inhomogeneity of the B0. I'm going to ask to you if there's any normalization way of this image because when I execute the recon-all command I foud many segmentation errors in this zone. Thaks for your help Greetings Leonardo

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recon-all with nifti
by Christophe Chênes 14 Apr '10

14 Apr '10

Hi, I'd like to launch recon-all with a nifti input file and get a nifti file in output... Do you know how can I do that? Thanks in advance! Chris'

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Which way is better for mapping automatic segmentations
by liang wang 14 Apr '10

14 Apr '10

Hi FSusers, I am engaging to map automatic segmentation image (eg. aparc.a2009s+aseg.mgz) to raw functional space. According to the instructions from the FreeSurfer website, I found that there were two ways below to do it. However, the results from both methods are different and attached. Let me say BNC006 is a subject under $SUBJECTS_DIR (here /drive3/TEST). The functional data has been processed using FSL and found in bold.feat directory. *# one way* (red images in the attached picture) $ bbregister --mov example_func.nii.gz --bold --s BNC006 --init-fsl --reg register.dat $ mri_label2vol --seg BNC006/mri/aparc.a2009s+aseg.mgz --temp example_func.nii.gz --reg register.dat --fillthresh 0.5 --o BNC006 .aseg-in-fun.nii.gz *# anther way* (blue images in the attached picture) $ reg-feat2anat --feat /drive3/TEST/BOLD/bold.feat --subject BNC006 $ aseg2feat --feat /drive3/TEST/BOLD/bold.feat --aseg aparc.a2009s+aseg cd /drive3/TEST/BOLD/bold.feat/reg/freesurfer *BNC006 .aseg-in-fun.nii.gz* and *aparc.a2009s+aseg.nii.gz* are outputs from the first and second one, respectively. Does anyone give me some suggestion about which method is suitable to my situation. Best, Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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a question about mri_robust_template
by Guang Zeng 13 Apr '10

13 Apr '10

Hi, there, I have a question about mri_robust_template, I have a binary brainmask for each time point, I'd like to create a binary norm_template.mgz using mri_robust_template command. Has mri_robust_template an option to do nearest interpolation ? Thanks! Guang _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

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skull strip error
by Dana W. Moore 13 Apr '10

13 Apr '10

Hi everyone, I am using freesurfer version 4.5.0, and have just gotten an error message that I have never received before. The end of the recon-all script is pasted below. what does this mean? #@# Skull Stripping Mon Apr 5 15:06:52 EDT 2010 /home/fs01/kab2003/FS/133_S_0525/mri mri_watershed -T1 T1.mgz brainmask.auto.mgz Mode: T1 normalized volume ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C *************************WATERSHED************************** Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 20676 Find the largest 110-component... heap usage = 128720 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 6553 voxels first estimation of the COG coord: x=124 y=177 z=184 r=110 first estimation of the main basin volume: 5673266 voxels mri_watershed Error: Problem with WM_MIN too small Linux compute-3-14.v4linux 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Apr 5 15:06:54 EDT 2010 Thanks, Dana

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mri_label2vol: how to make the opposite direction?
by John Gelburg 13 Apr '10

13 Apr '10

Hi, I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label? Thanks for help, John

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Colortable in annotations
by Dankner, Nathan (NIH/NIMH) [F] 13 Apr '10

13 Apr '10

Hi all, I am running cluster corrections on data and attempting to display the resulting cluster maps. Is it possible to make all of the clusters in an annotation the same color? And if so, how? As it stands now, all of the clusters are given a different color. Thanks for your help, Nathan

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Job Announcement - Research Assistant in Brain Imaging
by Victoria Williams 13 Apr '10

13 Apr '10

Job Announcement: Research Assitant in Brain Imaging Boston, MA, USA Full time research assistant positions are available in structural and functional imaging of several clinical conditions including degenerative brain changes in individuals with neurological diseases, traumatic brain injury, and post-traumatic stress disorder using magnetic resonance imaging (MRI). The technician will be responsible for processing and analyzing MRI images, as well as for running analyses combining MRI data with neuropsychological, behavioral and other health associated data. The technician will also be trained in operation of the MRI scanner, and for maintaining and updating datasets. In addition, the research assistant will have the opportunity to take advantage of several educational opportunities, such as seminars and talks, in the Boston area. Candidates must have a high degree of computer literacy and be willing to learn to use our locally developed MRI analysis software. A long-term interest in neuroscience, neuropsychology, clinical psychology, or patient care is preferred, and a two-year commitment is required. Some knowledge of basic statistics is a plus. Applicants should send a resume and contact information for two references via email to David Salat: salat *at* nmr.mgh.harvard.edu with "RESEARCH ASSISTANT" as the subject line. More information about the Martinos Center can be found at http://www.nmr.mgh.harvard.edu/. Information about technical aspects of this work can be found at http://surfer.nmr.mgh.harvard.edu/fswiki.

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Freesurfer April 2010