Freesurfer January 2011

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

trgicoorder flag in mri_surf2surf
by Joakim Vinberg 02 Jan '11

02 Jan '11

Hi everybody, I am interested in doing sub-sampling of functional data for some new analyses. Just about the only reference I can find to sub-sampling of data in FreeSurfer is in mri_surf2surf, which has an optional flag trgicoorder. The comment for this flag is: "This specifies the size of the icosahedron according to the formula #vertices=10*4^n+2. In general, it is best to use the largest size available." It would seem that I might be able to use this flag in order to sub-sample surface data by using a smaller n (it seems as if the default for fsaverage is 7 according to the specified formula). Is this correct? Are there any particular guidelines to n? Other surfaces have a variety of vertices, so it seems that n does not have to be an integer? If I computer a surface of functional data for a given subject with a specific 'n' and resulting nVertices, should I also calculate an according anatomical surface with the same number of vertices for display and analysis? Thanks! Joakim

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matlab loading problem (mkcontrast, selxavg3-sess)
by Katherine Sledge Moore 02 Jan '11

02 Jan '11

I am having trouble with the interface between freesurfer and matlab. When I run mkcontrast-sess and selxavg3-sess, matlab opens, but nothing happens (the script does not finish.) When I force it to quit, I get the error "-display: Command not found." In both mkcontrast and selxavg3-sess, the command to call matlab is something along the lines of "matlab -display iconic". Any thoughts as to why the "-display iconic" part is not being interpreted? Katherine Sledge Moore Postdoctoral Associate Visual Cognitive Neuroscience Laboratory Yale University http://camplab.psych.yale.edu/ http://pantheon.yale.edu/~khs8

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the usage of mri_surf2vol program
by qizhu wu 02 Jan '11

02 Jan '11

Dear all, Continue with my previous question in "To use the file thickness.mgh outside Freesurfer". Thanks for Doug's recommedation to use the mri_surf2vol program to convert mgh files into image format, such as NIFTI. But I failed due to wrong setting on several arguments: 1, '--volreg': I do not understand what file it requires. It's declared in --help that "Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume". But I am only dealing with the structural volumes, and has this file been created in any step during the previous processing? Or could anyone tell me clearly how to set this argument? 2, --surfval: if only pthname rather than single file is allowed as input here? 3, --template: couldI use mni305.cor.mgz, or just left these optional arguments empty? thanks in advance. Qizhu Wu

3 2

saving an external mesh in RAS coordinates
by Micheli, C. 01 Jan '11

01 Jan '11

Hi everybody, a very happy new year, with the hope 2011 will bring us near to our goals. I have a very simple question about surfaces in freesurfer. As i posted previously, i am trying to match white matter surface RAS coordinates with the corresponding anatomical volume. My attempt is to save an externally tessellated mesh (in scanner voxel coordinates) into RAS coordinates which match the volume. 1 - I first save the MRI T1 volume with save_mgh routine (i get the info about the vox2ras matrix by doing mri_info --vox2ras mri_file.nii) 2 - Then i save the surface (after transforming the voxel coordinates with the same vox2ras matrix used before for the volume) with write_surf 3 - Then i visualize volume and surface together with the tkmedit tool. Even if surface and volume seem to have correct projection alignment (coronal is coronal for both) there is evidently a mismatch in the superimposition of mesh and volumetric structures. The volume dimensions are 256X256X192 and is a monkey brain. Any suggestion to get me out of this local minimum? Greeting to everybody and congratulations for the nice toolbox Cristiano

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Freesurfer January 2011