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 <fis...@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
> >
> >
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> --
> Abigail C. McNulty
> Stanford University Class of 2018
> B.A. Candidate in Bioengineering
> Stanford Women's XC/ Track and Field
>
>
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