[Freesurfer] flat surfaces and negative indices

Dear freesurfer experts, I'm curious to understand the meaning of negative indices in flatten surfaces. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

[Freesurfer] Beginner Question on registration process

Hi all, I'm a new freesurfer user and I've a small question for you all. Which the faster and reliable way to map a list of points into the freesurfer geometrical space? I've already read the pdf/ppt but there's no suggestion in there about which command should be used (if any). I've read about m

Re: [Freesurfer] Beginner Question on registration process

e DICOM share the same space. > > doug > > > On 1/21/11 9:08 AM, Gabriele Arnulfo wrote: > > Hi all, > > MRI, in this context, i was considering the original DICOM T1 MRI space > before the conversion to 001.mgz file. Is your suggestion still the right > way to sol

[Freesurfer] Which surface to mesh_vertex_nearest

Hi again, looking in previous emails in the list i found that the best way to find the nearest vertex number to a certain point is by using the matlab script mesh_vertex_nearest. So far I've used it with input parameters: the vertices read through read_surf(rh_pial) and a matrix of Cartesian Coord

Re: [Freesurfer] Which surface to mesh_vertex_nearest

> what are you trying to accomplish? The "right choice" depends on your > goals. > > cheers > Bruce > > On Tue, 25 Jan 2011, Gabriele Arnulfo wrote: > > Hi again, >> >> looking in previous emails in the list i found that the best way to find >

Re: [Freesurfer] Which surface to mesh_vertex_nearest

gt; idea how deep the electrodes are? The white might be best as it will > minimize the chances of erroneously assigning the electrode to the wrong > bank of a sulcus. > > > cheers > Bruce > > > On Tue, 25 Jan 2011, Gabriele Arnulfo wrote: > > Hi Bruce, >

[Freesurfer] mesh_vertex_nearest and white matter segmentation

Hi list, I've got to questions: 1) mesh_vertex_nearest matlab script takes the vertices from a surface a matrix of points in 3D Cartesian coordinates system. Is it correct if I choose points in the Scanner RAS Space as input for this script? I cannot figure out by the description of the tool. 2)

[Freesurfer] Visualize contacts inside brain volume with overlay image

Dear freesurfer experts, I was wondering if there's an easy way to visualize contacts of intra-cerebral electrodes within tkmedit. Here's the scene: I've got a volume, which contains a white cross for each contacts on some linear intra-cerebral electrodes. This volume is in nifti format

Re: [Freesurfer] Visualize contacts inside brain volume with overlay image

t; rest of the volume transparent. You could also try using freeview, which > is far more flexible. > > cheers > Bruce > On Thu, 21 Apr 2011, Gabriele Arnulfo wrote: > > > Dear freesurfer experts, > > I was wondering if there's an easy way to visualize contacts

[Freesurfer] freeview and control points label

ntrol points in order to easily navigate through the brain volume and find the expected contact without inserting the ras coordinate to a cursor position. Is there a smart way to do this? Thank in advance, -- Gabriele Arnulfo PhD Student Bioengineering Department of Systemistic, Telematic

[Freesurfer] nearest mesh vertex

e reliable way to compute automatically the nearest vertex for a specified control point? Thank in advance, -- Gabriele Arnulfo PhD Student Bioengineering Department of Systemistic, Telematic and Informatic University of Genoa, Italy Viale Causa 13, 16100 __

Re: [Freesurfer] nearest mesh vertex

ive search > wouldn't be too bad. > On Thu, 5 May 2011, Gabriele Arnulfo wrote: > > > Sorry here it is. > > > > I need to find the nearest vertex through a script since the contacts > > are 150 in average for each patients and any manual computation is &

[Freesurfer] Flattened surface visualization using matlab

Dear freesurfer experts, I've surfed the web looking for some example on how to visualize the flattened surface using matlab, but none has appeared so far. Does this task have been already addressed by someone? Cheers, -- Gabriele Arnulfo PhD Student Bioengineering Department of System

[Freesurfer] freeview load fiducials from 3DSlicer

Hi guys, I've got a list of fiducials (fcsv) from 3DSlicer, Is there a way to import them within freeview? Those points look like label,x,y,z,[flag],[flag] i.e. P,57.799,-49.1799,13.07,1,1 P,-4.05607,-47.1519,8.93645,1,1 thank in advance. g. ___ F