[Mne_analysis] convert MRI to .fif

[dgw]

Yes, plus you can use the excellent mne_organize_dicoms to avoid the
persnickity unpacksdcmdir.

hth
d

On Wed, Apr 13, 2016 at 3:49 PM, Jon Houck <jhouck at unm.edu> wrote:
> 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.
>
> Jon
>
>
> 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
> http://casaa.unm.edu/jhouck.html
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