[Mne_analysis] Dicom organization

[Isaiah C. Smith]

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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