[Mne_analysis] setting up MNE

[Alexandre Gramfort]

Hi Vitória,

MNE needs the freesurfer reconstruction from your subject.

you can download the MNE sample dataset for an example.

then a standard pipeline is available at:

http://martinos.org/mne/command_line_tutorial.html

make sure your environment variables :

http://martinos.org/mne/manual/list.html?highlight=subjects_dir#user-environment

are properly setup.

HTH

cheers,
Alex

On Wed, Nov 16, 2011 at 8:43 AM, Vitória Piai <V.Piai at donders.ru.nl> wrote:
> Hi,
>
> I've never used MNE before and I'm running into a very simple problem.
> When creating the source space, I get the error "Could not find the MRI data
> directory ..."
>
> export MNE_ROOT=<MNE directory>
> cd $MNE_ROOT/bin
> . ./mne_setup_sh
> export SUBJECTS_DIR=<Subject directory>
> export SUBJECT=Subject01
>
> Since I'm using MNE from a pipeline of Fieldtrip, I have my data
> preprocessed in Freesurfer. I now have to the same SUBJECTS_DIR directory as
> I had it for Freesurfer.
>
> On another Wiki page, I found the following:
>
> MNE requires to set up the same environmental variables as FS. It is because
> MNE will look for the MRI data that is processed by FS (therefore, it will
> look for directories that are made by FS). Therefore, SUBJECTS_DIR
> environmental variable should refer to that directory where the anatomical
> data is (pre-processed by FS), and SUBJECT should refer to the sub-directory
> of SUBJECTS_DIR where the anatomical data is from the person whose data is
> analyzed.
>
> <MNE ANALYSIS DIR>/subjects/<subject's name>: contains the output from FS
>
> I thought I had it right but I'm a bit confused now. What does MNE need
> exactly? Does it need a .mri file as well? Or only the output from
> freesurfer?
> I can't really figure out where it goes wrong from the MNE tutorial
> either.
>
> Thanx a lot, Vitória
>
> --
> Vitória Piai
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognition
> Radboud University Nijmegen
> Montessorilaan 3, B.01.05
> 6525 HR Nijmegen
> The Netherlands
>
> Email : V.piai at donders.ru.nl
> Phone : +31 24 3612635
> www.vitoriapiai.com
>
> ** Please consider the environment - do you really need to print? **
>
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