Re: [Freesurfer] Making a patch of area A

Hi Daniel, don't use Euclidean distance. Use the length of the great circle connecting each point to the central vertex on the ?h.sphere surface. Bruce On Tue, 8 Mar 2005, Daniel Goldenholz wrote: Doug I was thinking of trying something like that. If I took all vertices which are a radius M or

Re: [Freesurfer] Making a patch of area A

Doug I was thinking of trying something like that. If I took all vertices which are a radius M or less from my centriod, aren't I basically done? (M is defined as the maximum euclidean distance between the centroid on the sphere and the ring of outer vertices. If my surface distance max is calle

Re: [Freesurfer] Making a patch of area A

Hi Daniel - Well it seems to me that you're almost there already. A Dijkstra algorithm is the ideal engine to determine radial paths from a central node - I suspect you just need to tune the graph cost function to take the Euclidean distance between nodes (as opposed to the logical distance) in

Re: [Freesurfer] Making a patch of area A

You might try starting off with the ?h.sphere. It's easy to parameterize these things on the sphere. The sphere, of course, has some metric distortion, but if the patch is small, it might not be to bad. Once you've identified the vertices in the patch (or maybe a slightly bigger patch), then you c

[Freesurfer] Making a patch of area A

Hi. I have a graph theory question: I would like to make a definition of a particular patch of cortex, that has a centroid at position (x,y,z) and has a total area of A. I thought that this was going to be somewhat hard, but I soon learned that it is very hard. First, I found some code for the

Re: [Freesurfer] Convert procedure

Hi Luca, I'll leave this for Doug. Bruce On Tue, 8 Mar 2005, Luca Roccatagliata wrote: Dear Bruce, thanks for your suggestion. I tried that command (mri_convert slice.dcm $SUBJECTS_DIR/$subject/mri/orig), after entering the folder containing .dcm files, but at first it didn't recognize the file typ

Re: [Freesurfer] Convert procedure

Dear Bruce, thanks for your suggestion. I tried that command (mri_convert slice.dcm $SUBJECTS_DIR/$subject/mri/orig), after entering the folder containing .dcm files, but at first it didn't recognize the file type. I added the option -it dicom, then it looked for a dicom file but it gave this erro

Re: [Freesurfer] Expert Preferences

mri_segment -wm_low -gray_hi On Tue, 8 Mar 2005, Marie Schaer wrote: The ones in csurf-Expert Preferences Settings Menu, under WMFilter: white low limit and gray high limit. Thanks, Marie Quoting Bruce Fischl <[EMAIL PROTECTED]>: what preferences exactly? On Tue, 8 Mar 2005, Marie Schaer wro

Re: [Freesurfer] Expert Preferences

The ones in csurf-Expert Preferences Settings Menu, under WMFilter: white low limit and gray high limit. Thanks, Marie Quoting Bruce Fischl <[EMAIL PROTECTED]>: > what preferences exactly? > > On Tue, 8 Mar 2005, Marie Schaer wrote: > > > > > Hi everybody, > > > > I am using Freesurfer to

Re: [Freesurfer] Expert Preferences

what preferences exactly? On Tue, 8 Mar 2005, Marie Schaer wrote: Hi everybody, I am using Freesurfer to measure the cortical thickness, and I was wondering if there was any way to specify the WMFilter Expert Preferences when running recon-all -stage1 from the commandline? Thanks in advance, Marie

[Freesurfer] Expert Preferences

Hi everybody, I am using Freesurfer to measure the cortical thickness, and I was wondering if there was any way to specify the WMFilter Expert Preferences when running recon-all -stage1 from the commandline? Thanks in advance, Marie Schaer ___ Frees