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.
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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Leonardo Chesi