[Mne_analysis] Dicom organization

Isaiah C. Smith Isaiah.C.Smith.17 at dartmouth.edu
Mon Aug 4 15:44:20 EDT 2014
Search archives:

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?

Isaiah
On Aug 4, 2014, at 11:53 AM, Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr<mailto: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

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140804/e42d48ee/attachment.html 


More information about the Mne_analysis mailing list