[Mne_analysis] convert MRI to .fif
Krieger, Donald N.
kriegerd at upmc.edu
Wed Apr 13 17:32:11 EDT 2016
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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