Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

segmentation errors
by Nicola Hobbs 05 Aug '08

05 Aug '08

Hello all, We've noticed some errors in the wm and pial segmentations (see t1.png) even though the wm.mgz seems to be correct (see wm.png). Could you advise us on the best way to correct these errors? Many thanks, Nicola -- Nicola Hobbs Dementia Research Centre National Hospital for Neurology and Neurosurgery Queen Square London WC1N 3BG +44 (0)845 155 5000 x723839

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NITRC website
by Nick Schmansky 05 Aug '08

05 Aug '08

Of potential interest to people on this list is the NITRC website: http://www.nitrc.org/ "The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) is funded by the National Institutes of Health Blueprint for Neuroscience Research. NITRC facilitates finding and comparing neuroimaging resources for fMRI and related structural analyses. NITRC collects and points to standardized information about tools, making the task of finding and comparing them easier than before. The site can help you find the right fMRI tool or resource and help you decide whether it can help in your research." FreeSurfer is listed in the site: http://www.nitrc.org/projects/freesurfer/

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Floating exception (core dumped)
by Juranek, Jenifer 05 Aug '08

05 Aug '08

Hi, Running fsv405 on RHEL4 (64bit) and have encountered the following error after executing recon-all -all: Floating exception (core dumped). Did not encounter this error using fsv401 on the same box. See below for the standard output to screen. Any ideas? Many Thanks, Jenifer [jjuranek@localhost subjects]$ recon-all -all -s PC_011_APO143_2mo INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwx--- 1 jjuranek root 2271789 Jul 25 07:15 /usr/local/freesurfer/subjects/ PC_011_APO143_2mo/scripts/recon-all.log Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux Floating exception (core dumped) #-------------------------------------------- #@# MotionCor Tue Aug 5 11:38:42 CDT 2008 Found 1 runs /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig/001.mgz /usr/local /freesurfer/subjects/PC_011_APO143_2mo/mri/rawavg.mgz /usr/local/freesurfer/subjects/PC_011_APO143_2mo mri_convert /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/rawavg.mgz /us r/local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/rawavg.mgz /usr /local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig.mgz --conform

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Version 4.0.3 download
by Matt Clarkson 05 Aug '08

05 Aug '08

Hi there Apologies if this has been asked before, or is obvious. One of our machines has FreeSurfer version 4.0.3, and I would like to install the same version on another machine, but its a different architecture. Please can anyone tell me if, or where I can find the downloads for version 4.0.3. I need something like: freesurfer-Linux-rh9-stable-pub-v4.0.3-full.tar.gz I don't really want to take the risk of changing the FreeSurfer version when some people in the group are halfway through various projects. Many thanks in advance. Matt -- Matt Clarkson Senior Research Associate Dementia Research Centre UCL Institute Of Neurology Queen Square London WC1N 3BG m.clarkson(a)ucl.ac.uk Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066

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Segmentation errors
by Nicola Hobbs 05 Aug '08

05 Aug '08

Hello all, We've noticed some errors in the wm and pial segmentations (see t1.png) even though the wm.mgz seems to be correct (see wm.png). Could you advise us on the best way to correct these errors? Many thanks, Nicola > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > -- Nicola Hobbs Dementia Research Centre National Hospital for Neurology and Neurosurgery Queen Square London WC1N 3BG +44 (0)845 155 5000 x723839

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Sample size
by Claus Reinsberger 04 Aug '08

04 Aug '08

Hi Freesurfers, could anybody tell, whether there is a way for a proper estimation of a sample size to plan a prospective study (cortical thickness measurements using qdec)? I suppose I can only refer to other publications examining a similiar cohort using freesurfer - is that right? I appreciate your help very much, Claus

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question about image size
by Lindsay Casmaer 01 Aug '08

01 Aug '08

Hello all, I am looking at using the Freesurfer white matter images in conjunction with PET PIB analysis. When I compare the wm.mgz image with the T88 image in Analyze, the wm image appears almost 10 percent smaller in both height and width when compared with the wm in the T88 mprage. Are the images padded to create the wm.mgz? Is there any transformation to expand the wm image back to the native space? Thanks, Lindsay

2 1

importing vertices and applying path_new_path_from_marked_vertices
by Aaron Shmookler 31 Jul '08

31 Jul '08

Hello, Here's what I did: 1) mris_convert ?h.inflated file.asc 2) extract vertices of interest into file2.asc Here is what I want to do: I want to import the vertices from file2.asc into tksurfer and apply the *path_new_path_from_marked_vertices *function so that I can then create a label. How might I do this? Thanks, Aaron

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3.0.2
by p.s.bjerkan＠studmed.uio.no 31 Jul '08

31 Jul '08

Hi! Need the centos4 x86_64 version of 3.0.2 Can´t find it on the ftp server or on the wiki. Thanks! Petr

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again: qdec error
by Dorit Kliemann 30 Jul '08

30 Jul '08

Dear all, I wanted to open qdec for the first time and experienced an error that was posted some days ago... ( RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow ; Juranek, Jenifer ) " ERROR: In /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 219 vtkXOpenGLRenderWindow (0x49220f0): Could not find a decent visual" In contrast to the previously reported incident, I was finally able to open qdec by just clicking 'ok' on 3 of those exact same error messages. Still - I could not read in any .dat files..... I tried to follow the advice given in the previous threat " In the file /etc/X11/xorg.conf, within the section titled Section "Module", make sure this line exists: Load "glx" You might need to have your administrator perform this change, as it requires root access. You will have to restart your X server after making this change (Ctrl-Bksp)." ..but I don¹t have the referred file in the X11 folder (xorg.conf). FYI, I¹m using the latest Freesurfer version and for a colleague of mine qdec works without having that xorg.conf file..... It is possible that there is any other reason for the qdec error? Thanks, Dorit

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