Freesurfer March 2008

freesurfer@nmr.mgh.harvard.edu

55 participants
81 discussions

obtaining older version of freesurfer
by Glenn Lawyer 21 Mar '08

21 Mar '08

Dear FreeSurfer team, Do you still make older versions of FreeSurfer available on your website? I'm specifically looking for a v3 stable release, but my situation may not be unique.

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Question re: extracting functional data from cortical ROIs
by Dan Dillon 20 Mar '08

20 Mar '08

I have a question about extracting functional data from structurally defined cortical labels. Here's what I'm doing: 1) Run a gammafit analysis; 2) Define cortical ROIs by using mri_annotation2label to make labels from aparc.annot; 3) Define sub-cortical ROIs by using mri_cor2label to make labels from aseg.mgz; 4) Extract functional data from labels using func2roi-sess; 5) Summarize the data with roisummary-sess. I usually view the cortical ROIs on the inflated (or pial) surface and the subcortical ROIs in the volume, and they usually look great. But when I view the cortical labels in the volume, they seem to consist of a 1-voxel thick strip hugging the white matter; they don't seem to cover the gray matter at all. Does this mean that I am extracting functional data from a 1-voxel thick strip (!), or am I just mis-understanding something about how a cortical label appears in the volume? Also, I know that "white" is the default surface in mri_annotation2label, but if I switch to "pial", make a label, and view it in the volume, it still looks like a 1-voxel thick strip, just around the outside edge of the gray matter (instead of around the inside edge if I use "white" as the surface). My simple mind wonders why these cortical labels-which look great on the inflated brain-don't cover the region between the pial and white surfaces (i.e., the gray matter) in the volume. Am I making a basic error here? If so, what do I need to do to extract functional data from cortically-defined ROIs? I am running version 4.0.2. Thanks! Dan D.

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Question about functional analysis
by lan lin 19 Mar '08

19 Mar '08

When we use freesurfer to do functional analysis(such as PET), do we need to account for global mean? thanks

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Question about slopes
by Jerry Yeou-Wei Chen 19 Mar '08

19 Mar '08

Hello, The attached image shows a plot generated from a design with one continuous variable (gender) and three continuous variables (called N, E, P), analyzed using the "old" method via command line rather than QDEC. For mri_glmfit, the DODS option was used and the contrast was 0 0 1 -1 0 0 0 0 (to compare the relation between N and thickness, in females versus males). I am wondering why the fitted lines seem to be so far "off" from the actual data points. Could anyone please shed some light on this issue? Please let me know if you need any more information about our analysis. Thanks, - Jerry

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mri_glmfit...
by Cameron Ellis 19 Mar '08

19 Mar '08

Hi all, Does mri_glmfit run to correlate volume with a particular measure identify clusters on a voxel by voxel basis or does it compare the aseg volumes of the different subcortical structures? Thanks, Cameron

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QDEC limited regressors
by Jerry Yeou-Wei Chen 19 Mar '08

19 Mar '08

Hello, I would like to know why we are limited to 4 regressors in the design specification within the QDEC GUI. If I understand correctly, there is no such limitation in the "old" method (via command line). Thanks, - Jerry

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Job Announcement, University of Minnesota
by Bryon Mueller 19 Mar '08

19 Mar '08

Hi, I'd like to pass this job announcement on to the Freesurfer list. This is an opportunity to join a great imaging community at the University of Minnesota. Best, Bryon Mueller -------------- NeuroImaging Staff Scientist Position Opening. The College of Liberal Arts invites applications for a Neuroimaging Staff Scientist who will 1) assist with establishing new acquisition and data analysis methods for experienced and new investigators, and 2) assist in training graduate students in neuroimaging data collection and analysis. This position will offer technical support and training for faculty, staff and students acquiring fMRI data, primarily on a 3 Tesla Siemens scanner but also on a 7T Siemens scanner. The research associate will also work with the computer resource group at the University of Minnesota's Center for Magnetic Resonance Research to help implement new data acquisition and analysis techniques and help new researchers establish data analysis streams and to make state-of-the-art techniques available to the broader research community. If you have further questions, contact Cheryl Olman at caolman(a)umn.edu. To apply go to: https://employment.umn.edu/applicants/jsp/shared/frameset/Frameset.jsp?time…

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loading previous qdec analysis
by Michael Harms 18 Mar '08

18 Mar '08

Hello, Having previously saved a qdec-based analysis (i.e., "Design Name"), is it possible to reload/review that analysis within qdec? (Is "Load Project File" involved somehow?) thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Creating a Volume from the finished Pial Surface
by Cochrane Jamison 18 Mar '08

18 Mar '08

Hello. I am still very new to freesurfer. I have finished running a complete recon all process on one mri. I used a very good scan, which produced great results from freesurfer. However, I am having trouble producing some usable output. I want to create a volume from the finished pial surface so that I can load it into another program for dipole analysis. I have read through the archives and come across the command mri_surf2vol that seems to be able to do what I am trying to do. I am having problems with is though. Here is where I started: MEG-PC:~/freesurfer/subjects/C0668_Duck/mri> mri_surf2vol --hemi lh --template ../orig/001.mgz --outvol left_filled_pial.img --fillribbon --surf pial gdiagno = -1 A surface value path must be supplied In another post, I saw where the user had used the lh.thickness for the surface values, so I tried the same and got this: MEG-PC:~/freesurfer/subjects/C0668_Duck/mri> mri_surf2vol --hemi lh --surfval ../surf/lh.thickness --template ../orig/001.mgz --outvol left_filled_pial.img --fillribbon --surf pial gdiagno = -1 A volume registration file must be supplied I have read the help file about tksurfer2 and creating a volume registration file, but I cannot exactly figure out what all I need for inputs, and what kind of output I want exactly. I know this may not be as much detail as you need, so please let me know if you have any questions. Thank you for the help. William

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qdec display problem
by Michael Harms 18 Mar '08

18 Mar '08

Hello, Has anyone reported, or have you experienced, the following issue with the qdec surface display: As soon as I left click on the surface (as if to rotate it), the display seems to get "confused" about how to render the surface properly -- see attached jpeg for a visual. If I select an alternative surface among 'inflated', 'pial', or 'white', the surface is temporarily displayed correctly until I left click on it again. I'm using FS v4.0.2 from the 32-bit CentOS build. thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Freesurfer March 2008