Hello,
I am trying to segment a MRI brain in order to create a mesh of the image into finite elements, but I am very new with Freesurfer/Freeview and am not familiar with the tools. So far, I have only uploaded brain.mgt from the bert file that comes with the program. If I wanted to mesh this brain, how should I proceed? The online tutorials have confused me especially since I am not sure if I am supposed to be using the terminal or the command window for a lot of the code commands.
Any help would be appreciated.
Thanks!
Abbie McNulty
Hi Abbie
what are you trying to create a mesh of? We supply meshes for the gray/white interface and for the pial surface. We supply voxel segmentations of lots of other things that you could mesh, but we don't by default.
cheers Bruce On Mon, 27 Jun 2016, Abbie McNulty wrote:
Hello, I am trying to segment a MRI brain in order to create a mesh of the image into finite elements, but I am very new with Freesurfer/Freeview and am not familiar with the tools. So far, I have only uploaded brain.mgt from the bert file that comes with the program. If I wanted to mesh this brain, how should I proceed? The online tutorials have confused me especially since I am not sure if I am supposed to be using the terminal or the command window for a lot of the code commands.
Any help would be appreciated.
Thanks!
Abbie McNulty
-- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field
Hi Bruce,
I am trying to create a mesh of the MRI scans, eventually with imported scans, but for now just using the information available through the software. How do you work these voxel segmentations? I'm just very new with the software.
Say I import an MRI scan, and I want to cortically segment it in order to create a mesh of the volume. What are the steps to do this and how do I follow through with each step? I tried to watch the youtube tutorials on the Freesurfer youtube, but since they are slides informing of what Freesurfer can do and not quite a play-by-play interaction of Freeview, I am stuck.
Thanks
Abbie
On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Abbie
what are you trying to create a mesh of? We supply meshes for the gray/white interface and for the pial surface. We supply voxel segmentations of lots of other things that you could mesh, but we don't by default.
cheers Bruce On Mon, 27 Jun 2016, Abbie McNulty wrote:
Hello, I am trying to segment a MRI brain in order to create a mesh of the image into finite elements, but I am very new with Freesurfer/Freeview and am
not
familiar with the tools. So far, I have only uploaded brain.mgt from the bert file that comes with the program. If I wanted to mesh this brain,
how
should I proceed? The online tutorials have confused me especially since
I
am not sure if I am supposed to be using the terminal or the command
window
for a lot of the code commands.
Any help would be appreciated.
Thanks!
Abbie McNulty
-- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Essentially, once segmentation is achieved, how do you mesh the scans?
On Mon, Jun 27, 2016 at 3:41 PM, Abbie McNulty amcnult1@stanford.edu wrote:
Hi Bruce,
I am trying to create a mesh of the MRI scans, eventually with imported scans, but for now just using the information available through the software. How do you work these voxel segmentations? I'm just very new with the software.
Say I import an MRI scan, and I want to cortically segment it in order to create a mesh of the volume. What are the steps to do this and how do I follow through with each step? I tried to watch the youtube tutorials on the Freesurfer youtube, but since they are slides informing of what Freesurfer can do and not quite a play-by-play interaction of Freeview, I am stuck.
Thanks
Abbie
On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Abbie
what are you trying to create a mesh of? We supply meshes for the gray/white interface and for the pial surface. We supply voxel segmentations of lots of other things that you could mesh, but we don't by default.
cheers Bruce On Mon, 27 Jun 2016, Abbie McNulty wrote:
Hello, I am trying to segment a MRI brain in order to create a mesh of the
image
into finite elements, but I am very new with Freesurfer/Freeview and am
not
familiar with the tools. So far, I have only uploaded brain.mgt from the bert file that comes with the program. If I wanted to mesh this brain,
how
should I proceed? The online tutorials have confused me especially
since I
am not sure if I am supposed to be using the terminal or the command
window
for a lot of the code commands.
Any help would be appreciated.
Thanks!
Abbie McNulty
-- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field
Hi Abbie
you just use the recon-all script from the command line:
recon-all \ -i <path to 1 file in the correct dicom series> \ -sd <path to the directory that you store all your subjects> \ -s <identifier to give this subject> \ -all
this will take 5-20 hours and at the end will create and populate a directory tree with segmented volumes and surfaces cheers Bruce
On Mon, 27 Jun 2016, Abbie McNulty wrote:
Hi Bruce, I am trying to create a mesh of the MRI scans, eventually with imported scans, but for now just using the information available through the software. How do you work these voxel segmentations? I'm just very new with the software.
Say I import an MRI scan, and I want to cortically segment it in order to create a mesh of the volume. What are the steps to do this and how do I follow through with each step? I tried to watch the youtube tutorials on the Freesurfer youtube, but since they are slides informing of what Freesurfer can do and not quite a play-by-play interaction of Freeview, I am stuck.
Thanks
Abbie
On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Abbie
what are you trying to create a mesh of? We supply meshes for the gray/white interface and for the pial surface. We supply voxel segmentations of lots of other things that you could mesh, but we don't by default. cheers Bruce On Mon, 27 Jun 2016, Abbie McNulty wrote: > Hello, > I am trying to segment a MRI brain in order to create a mesh of the image > into finite elements, but I am very new with Freesurfer/Freeview and am not > familiar with the tools. So far, I have only uploaded brain.mgt from the > bert file that comes with the program. If I wanted to mesh this brain, how > should I proceed? The online tutorials have confused me especially since I > am not sure if I am supposed to be using the terminal or the command window > for a lot of the code commands. > > Any help would be appreciated. > > Thanks! > > Abbie McNulty > > -- > Abigail C. McNulty > Stanford University Class of 2018 > B.A. Candidate in Bioengineering > Stanford Women's XC/ Track and Field > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field
freesurfer@nmr.mgh.harvard.edu
-
Abbie McNulty -
Bruce Fischl