vol2surf won't work - that's for scalar maps. You need a tesselation I guess, which you can generate with mri_tesselate or mri_mc. If it's just for visualization though you could probably just load it into freeview and look at it as an isosurface of the volume.
cheers Bruce On Sun, 13 Jun 2010, Leonardo Chesi wrote:
Hi bruce, my goal is to obtain a 3D surface of the hippocampal region for a visual comparison with a manual segmentation made by a neuroradiologist. Today I managed to extract the volume with mri_binarize but I can't transform it in a surface that tkurfer can visualize. For that I try to use mri_vol2surf but I obtain a surface with 0 vertices. Can you help me?? Cheers Leonardo
-----Messaggio originale----- Da: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Inviato: domenica 13 giugno 2010 14.29 A: Leonardo Chesi Cc: freesurfer@nmr.mgh.harvard.edu; Ruopeng Wang Oggetto: Re: R: [Freesurfer] How means all the output file from a segmentation?
Hi Leonardo,
you just want to visualize it? Can you explain your goals a bit better? You could view it in freeview as an isosurface if you wanted. Ruopeng: is there wiki documentation for this?
cheers Bruce
On Sun, 13 Jun 2010, Leonardo Chesi wrote:
Hi Bruce, Thanks for your attention, Can you write for me a sample line where I want to compute a 3D volume of the hippocampal? And I can show it with tksurfer? Thanks Leonardo
-----Messaggio originale----- Da: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Inviato: sabato 12 giugno 2010 20.22 A: Leonardo Chesi Cc: freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] How means all the output file from a
segmentation?
Hi Leonardo,
the outputs are listed on our wiki. If you want to extract a single structure you can use mri_binarize using the indices in the $FREESURFER_HOME/FreeSurferColorLUT.txt file.
cheers Bruce On Sat, 12 Jun 2010, Leonardo Chesi wrote:
Hi, after the segmentation process, we obtain a lots of file that I can't understand what they represent. Infact I know the mean of the file
aseg.mgz
(that is a mask of the segmentation) and norm.mgz but for example I can't understand the difference between brainmask.mgz and brainmask_auto.mgz.
Can
you help me with a list of the output? And can I obtain the volume
rendering
of only one part of the segmented structure? (es. Hippocampal)??
Thanks for your help
Leonardo
The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.