[Mne_analysis] Dicom organization

[Alexandre Gramfort]

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