[Mne_analysis] convert MRI to .fif

Krieger, Donald N. kriegerd at upmc.edu
Wed Apr 13 17:32:11 EDT 2016
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Thank you very much, Jon.
I will try it first thing.

Best - Don

From: mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Jon Houck
Sent: Wednesday, April 13, 2016 3:49 PM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] convert MRI to .fif

If you have the Neuromag software there's the GUI-based dicom_access tool.  There was also a neuromag command line utility create_mri_sets (possibly only for HPUX?) to do this.

Since (presumably?) the usual Freesurfer --> MNE pipeline isn't appropriate in this case for some reason, there's another command line alternative.  First you'd use Freesurfer's unpacksdcmdir to extract the info about the dicom files from a directory (this produces a text file with information like run #, # of slices, etc), and then run it again using those extracted parameters to read the dicom files from the directory and convert them into an .mgh file (see https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData for a complicated example).  Then you can use the MNE-C command mne_make_cor_set to convert the .mgh file into a fif file (e.g., mne_make_cor_set --mgh mgh_input_file.mgh --out shiny_new_fif_file.fif).

All are a bit old school but should still work. Probably.


On Wed, Apr 13, 2016 at 11:40 AM, Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr<mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
this does not exist. Yet?

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Jon M. Houck, Ph.D.
Research Assistant Professor
Department of Psychology
Center on Alcoholism, Substance Abuse, and Addictions
University of New Mexico
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