Hello,

Just a couple more questions that would be great if you could answer in explanation form:

How do people develop finite element models from brain MRI?

How do people learn and implement the software on an example data set?

Abbie 

On Mon, Jun 27, 2016 at 6:37 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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
>       >
>       >
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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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--

Abigail C. McNulty

Stanford University Class of 2018

B.A. Candidate in Bioengineering

Stanford Women's XC/ Track and Field