setting up MNE

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1

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, Vit?ria

2

Hi Vit?ria,

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