Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

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

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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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set up of initial data directories
by Stephen Rose 30 Jul '08

30 Jul '08

Hi I am a new freesurfer user so I apologize in advance for the basic questions. If I already have my MPRAGE images in mgz format (i.e I don't need to convert the raw dicom data with mri_convert), what changes to the command line (below) do I need so that the all the correct data directories are initially set up (and not call mri_convert)? recon-all -i <path-to-structural> -s <subjid> When viewing the results of autorecon1 and 2 are all the surfaces and segmentation results shown in raw image space and not Talairach space? Thanks for your help Stephen A/Prof. Stephen Rose Principal Research Fellow Centre for Magnetic Resonance Centre for Clinical Research University of Queensland Brisbane, QLD, 4072 Australia Telephone: +61 7 33466101 Mobile: 0412023958 Fax: +61 7 33653833

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Screening specific subcortical structures in large samples
by Nicolas Cherbuin 29 Jul '08

29 Jul '08

Hi, I need to check the segmentation of a number of subcortical structures in a large sample. Is there a simple way to automatically display in a grid, say the segmented putamen of all subjects in one directory? Or alternatively to produce a picture file for this structure from a specific view point for all subjects which then could be quickly scanned for defects? I have used Slicer to view single structures in 3D and while it works very well it is too slow to look at many structures in hundreds of subjects.... Thanks for your help Nic

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How to do F test in fsfast?
by Zhen Zonglei 29 Jul '08

29 Jul '08

Dear fs/fsfast user: Would you please tell me how to do F test in fsfast? For example, I have 4 conditions, and want to test the 4x4 contrast matrix [1 0 0 0; 0 1 0 0; 0 0 1 0;0 0 0 1] with a F test. How should I use mkcontrast-sess or other commands to construct the contrast matrix and do F test? Thanks in advance. -- Zonglei Zhen, Ph.D Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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