[Mne_analysis] Dicom organization

[Denis-Alexander Engemann]

Hi Isaiah,


On Mon, Aug 4, 2014 at 9:44 PM, Isaiah C. Smith <
Isaiah.C.Smith.17 at dartmouth.edu> wrote:

>  Thanks Alex,
> I have completed the mne_watershed, and have the brain_surf, and other
> surfaces, as well as the head.fif. I used freesurfer and have the T1.mgz
> file, but I am confused as to the next step as I follow the cookbook. My
> original images are not in DICOM, but executive  document files. I see that
> the example that you sent went here next
>
> # Make high resolution head surface
> HEAD_FNAME=${SUBJECTS_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif
> if [ ! -f ${HEAD_FNAME} ];
> then
>     mkheadsurf -s ${SUBJECT}
>     mne_surf2bem --surf ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.seghead --id 4 --check --fif ${HEAD_FNAME}
> fi
>
> # Setup BEM
>
> to create the head surface. Or do I have to create the boundaries?
>
>
In cas you're already familiar with the MNE-Python suite (or not:) have a
look at

mne make_scalp_surfaces:
https://github.com/mne-tools/mne-python/blob/master/mne/commands/mne_make_scalp_surfaces.py

It generates a high-resulution head surfaces and 2 additional decimated
surfaces.
The medium surface is particularly satisfying and useful for coregistration.

Also have a look here:
http://martinos.org/mne/stable/auto_examples/plot_decimate_head_surface.html#example-plot-decimate-head-surface-py

Denis




>  Isaiah
>   On Aug 4, 2014, at 11:53 AM, Alexandre Gramfort <
> alexandre.gramfort at telecom-paristech.fr> wrote:,
>
> hi Isaiah
>
> I have a few questions of clarification below and one question that is
> preventing me from moving forward (under Kept Going).
>
> Previous Questions: I have the MRI data, but I am confused as to how to
> proceed with the mne_setup_mri for the brain, skull and scalp volume
> conduction models because the brain and T1 are the defaults. Do I need to
> add some other slices? And does the subject data need to be placed in
> /freesurfer/subjects for it to be read by MNE?
>
>
> you should be able to work with just a T1 file. You have run
> freesurfer on your T1 image
> then you generate the brain, skull and scalp surfaces with
> mne_watershed_bem
>
> see
>
>
> https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_anatomy_tutorial.sh
> https://github.com/mne-tools/mne-scripts/blob/master/spm_face/bootstrap.sh
>
> for demo scripts of anatomical pipeline.
>
> Kept Going:
> The folder just contains two empty folders after implementing
> mne_organize_dicom. It seems that the DICOM images are not being read
> properly. I do not know what is wrong here.
>
>
> I never use mne_organize_dicom or mne_setup_mri.
> Just recona-all on my T1 image eventually converted to .nii or .mgz
> with freesurfer
> mri_convert image.
>
> HTH
> Alex
>
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