Re: [Freesurfer] Cropping/slicing surfaces

2012-11-01 Thread Bruce Fischl
you should be able to use the read_patch.m that is in our matlab dir cheers Bruce On Thu, 1 Nov 2012, octavian lie wrote: Dear Bruce,   Thank you for your assist. I see the difference between patch and surface, but I would need to get he cut surface in matlab. I do not know how to set the rip

Re: [Freesurfer] Cropping/slicing surfaces

2012-11-01 Thread octavian lie
Dear Bruce, Thank you for your assist. I see the difference between patch and surface, but I would need to get he cut surface in matlab. I do not know how to set the ripflag=1 for x<0. Here is the code I use to upload surfaces in Matlab: function [vertex_coords, faces] = read_surf(fname) %QUAD_F

Re: [Freesurfer] Cropping/slicing surfaces

2012-11-01 Thread Bruce Fischl
It is no longer a surface - it is a patch and you need to load it that way. It's a different file format Bruce On Nov 1, 2012, at 1:22 PM, octavian lie wrote: > Dear Bruce, > One last question. I saved the cut surface as rh.inner-skull-surface > (original was rh.sub_inner_skull_surface) as a

Re: [Freesurfer] Cropping/slicing surfaces

2012-11-01 Thread octavian lie
Dear Bruce, One last question. I saved the cut surface as rh.inner-skull-surface (original was rh.sub_inner_skull_surface) as a patch, but when trying to see it in tksurfer, I get the following error message: tksurfer sub rh inner-skull-surface subject is sub hemi is rh surface is inner-skull-surf

Re: [Freesurfer] Cropping/slicing surfaces

2012-11-01 Thread Bruce Fischl
save it as a patch On Thu, 1 Nov 2012, octavian lie wrote: Thank you, Bruce. Is seems that the cut works well in tksurfer, however I am unable to save the cut surface, if I use save or save as, it saves the original (whole) surface. What should I do? Octavian. On Thu, Nov 1, 2012 at 11:49 AM,

Re: [Freesurfer] Cropping/slicing surfaces

2012-11-01 Thread octavian lie
Thank you, Bruce. Is seems that the cut works well in tksurfer, however I am unable to save the cut surface, if I use save or save as, it saves the original (whole) surface. What should I do? Octavian. On Thu, Nov 1, 2012 at 11:49 AM, Bruce Fischl wrote: > the easiest thing would be to copy it in

Re: [Freesurfer] Cropping/slicing surfaces

2012-11-01 Thread Bruce Fischl
Hi Octavian sure, define a sagittal cutting plane in tksurfer, or in matlab set ripflag=1 for all vertices with the x coord > 0 (or < 0) cheers Bruce On Thu, 1 Nov 2012, octavian lie wrote: Dear all,   Is there a way to crop a surface in FS, freeview or matlab? I have the inner_skull_surf

[Freesurfer] Cropping/slicing surfaces

2012-11-01 Thread octavian lie
Dear all, Is there a way to crop a surface in FS, freeview or matlab? I have the inner_skull_surface in BEM folder, and I want to see just the right half, akin to cropping along the A (RAS) axis from the left. This is in order to visualize the inside of the surface with some electrode applications