Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

fsaverage documentation
by Emily Rogalski 21 Mar '12

21 Mar '12

Hi All, I was looking for documentation on the fsaverage brain but I do not have permission to access the *Buckner40<http://surfer.nmr.mgh.harvard.edu/fswiki/Buckner40>page for notes on building fsaverage*. http://surfer.nmr.mgh.harvard.edu/fswiki/Buckner40 Has the information on this page been relocated? If so, can you point me to the new location? Thanks Emily -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

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Skull strip and white matter
by Vincent 21 Mar '12

21 Mar '12

Hi, I am having an issue where some dura remains behind after the skull strip and is being mistakenly classified as white matter. Since it is just dura, and not skull, would it be better to edit the white matter volume or should I start by adjusting the skull strip since occurs earlier in the recon-all processing stream? --Vincent

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interpreting cluster results
by Govindarajan, Koushik Athreya 21 Mar '12

21 Mar '12

Dear FS group, This may be a trivial question. Could not find answer in the archives. When Freesurfer outputs cluster summary files, it displays number of vertices (NVtxs). What is the size of each of these vertices. In other words, is there a standard correspondence between number of vertices and area of the cluster. Thanks Koushik

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Tkmedit question
by Antonella Kis 21 Mar '12

21 Mar '12

Dear All, I am trying to understand what should be my -fthresh and -fmax or -fmin and -fmax values while visualizing in tkmedit the significant map of uncorrected results so I can see all the clusters in this map. Further,I want to see what clusters from this map did not survived after corrections by multiple comparison for cluster voxel-wise equal 3. Thank you. Antonella

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Structural images quality
by Cícero Nardini Querido 21 Mar '12

21 Mar '12

Hi everyone, I am going to use FreeSurfer to analyze cortical thickness in some structural images. In order to generate the individual output, Freesurfer asks for 2 different input images. If I have two acquisitions from the same subject, but they present different degrees of quality (such as movement index), would it be better to use just one of them? Is there any problem in doing that? Also, is there a reliable index to assess the images level of movement before I use them on FreeSurfer? Thanks for that!

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tkmedit
by Richter, Julia 21 Mar '12

21 Mar '12

Hi freesurfer experts, I am trying to correct the pial surfaces for my cortical thickness analysis. I assume that I have to load my pial surface into tkmedit and that I have to specify the subject image_type and the absolute path. However, every time I specify the image_type of the subject, the terminal says that it cannot find the subject in the file I indicate, although I am of the opinion that it is the right file. Do I have to add something to the file where all the subject data is stored so that tkmedit can find the right data? Thanks for your help, Julia

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tksurfer crashes without error message
by Michelle Umali 20 Mar '12

20 Mar '12

Hi Freesurfers, I've been using Freesurfer for a while, and have had no trouble with launching tksurfer. But recently I have tried to view an inflated hemisphere of a subject I have had no problem viewing before. The window no longer opens. This the case for all of my subjects, with whom I have had no previous problems. Any suggestions would be most welcome. Thanks very much. Michelle Below is the terminal output. After this it just returns to the prompt without any error message.. /usr/local/freesurfer/subjects> tksurfer ld07 lh inflated subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=160638, faces=321272 surfer: double buffered window surfer: tkoInitWindow(ld07)

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freesurfer installation (fail)
by Daniël Höhle 20 Mar '12

20 Mar '12

Hello there, I''ve tried a couple installations of FreeSurfer as listed on the website. Though there seems to be a problem. Both linux tarballs seem to be designed for centos4, though that version is not supported anymore, so downloading is a pain, and accessing packages is out of the question. The same thing I encountered for Xubuntu 9.04. Freesurfer works, though, but it is (vritually) impossible to get information from a winfows network, because nfs-common needs to be installed, and since Xubuntu 9.04 is not supported anymore (a bit over a year now), I cannot install the packages needed to access data. Now I've downloaded Centos6 x86_32, I untarred the tarball, and I've set the environmental variables are listed. Though if I try the command "tkmedit bert orig.mgz" I get "/usr/local/freesurfer/tktools/tkmedit.bin: Command not found". I don't know whether I should try and tweak the Centos6 version, or whether freesurfer will not run on this OS all together. I got the impression that this project is still alive. Therefore I'd like to ask two questions: 1- can you, please, update the download section? FI virtual machine with Ubuntu 10.04, and tarballs and information for Centos6? 2- can you help me with installing this on Centos6? Kind regards, Daniël Höhle Scientific Programmer, Alan Turing Institute Almere, The Netherlands

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volume mapping
by Johnson 19 Mar '12

19 Mar '12

Hi This is Johnson, I am researcher at univ. of IL at chicago, I have a question regarding freesurfer: What is the transformation matrix that relates the freesurfer aparc+aseg space to the aparc+aseg-in-rawavg space, I am asking this question for the following reason: I have white matter fiber tracts in Diffusion space, I managed to transform it to aparc+aseg-in-rawavg space by registering the B0 to the brainmask-in-rawavg volume. Now I want to transform it to aparc+aseg space. thanks -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2(a)uic.edu

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FS 5.1: white matter holes in wm.mgz
by Adam Martersteck 19 Mar '12

19 Mar '12

Hey all, Problem: I am getting white matter ‘holes’ of varying sizes on the wm.mgz I’ve uploaded 6 images to show an example of such a hole that was created. It is the same wm hole from all 3 views shown in brainmask.mgz and wm.mgz. The album with all 6 images can be found at photobucket.com/FS51 Background: The hole appears within the first or second recon-all (after edits made) They are appearing in multiple subjects If they do appear in a subject - it is usually between 2-3 per volume I am using FS 5.1 on a mac (recon on a linux) I am performing pial/wm/cp edits I was curious if anyone had ever run into this error and a solution for avoiding it in the future. Thanks in advance for the help! Adam Martersteck Cognitive Neurology and Alzheimer’s Disease Center brain.northwestern.edu

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