[Mne_analysis] convert MRI to .fif

Jon Houck jhouck at unm.edu
Wed Apr 13 15:49:03 EDT 2016
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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> wrote:

> this does not exist. Yet?
> sorry
> A
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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
Albuquerque, NM 87131
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