Is there an mne tool which can convert an MRI to a .fif file .
I'm starting with .mgz and so can easily get to .nii and many other formats.
It's the conversion to .fif that's the problem.
Thanks - Don
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this does not exist. Yet?
sorry
A
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
Yes, plus you can use the excellent mne_organize_dicoms to avoid the
persnickity unpacksdcmdir.
hth
d
Thank you very much, Jon.
I will try it first thing.
Best - Don