[Mne_analysis] a junior question on mne_setup_source_space

[peng]

Thank you Martin for the help.
1. I re-run the command "mne_setup_forward_model" and it seemed working
this time (maybe I did not set the environment correctly). Sorry for the
confusion.
2. I tried with MNE_analyze GUI and it was not easy for me. But I saved
results from one subject successfully and it could be load by MNE_analyze.
However I wanted to read it in matlab to check the real contents (which I
assume is a structure with the transformation matrix). I failed with "x =
fiff_read_mri(fname, 0). It complained "Could not find MRI data"... Would
please let me know the function name to read and write *-src.fif file in
matlab?



On Wed, Mar 26, 2014 at 9:28 PM, Martin Luessi
<mluessi at nmr.mgh.harvard.edu>wrote:

> On 03/26/14 16:00, peng wrote:
> > Thank you for the answers.
> > 1. Surprisingly I did not find any files were generated/saved after
> > running mne_setup_forward_model.
>
> I assume there was an error, can you post the program output?
>
> > 2. I don't have a -trans.fif file. I tried to do it in GUI of
> > MNE_analyze, it was quite complicated. If I have a co-registered mri
> > file (generated by CTF software with .mri extension), can it be
> > converted to fif format? If not, I can read the 4x4 head2mri matrix via
> > matlab, can this information be written to fif format with certain tools
> > in MNE?
>
> There is also a coreg GUI in MNE-Python, have a look here
>
> http://www.slideshare.net/mne-python/mnepython-coregistration
>
> You could write a .fif file with the transform in Matlab, but it seems
> to me that this wouldn't be easier than using the coregistration tools
> in mne_analyze or MNE-Python.
>
> HTH,
>
> Martin
>
>
> > Thanks again!
> >
> >
> > On Tue, Mar 25, 2014 at 11:39 PM, Alexandre Gramfort
> > <alexandre.gramfort at telecom-paristech.fr
> > <mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
> >
> >     hi,
> >
> >     >  Some additional questions.
> >     > 1 After I ran mne_setup_forward_model, I have no feedback from the
> >     command
> >     > line, is it normal?
> >
> >     it should print that it saved a file to disk
> >
> >     > 2 I am using CTF data, thus I converted the .ds folder from CTF to
> fif
> >     > format with mne_ctf2fiff command, with option --infoonly. Here I
> >     only want
> >     > to get the Leadfield thus I suppose data is not necessary. However
> >     when I
> >     > try mne_do_forward_solution, it asked for mri description file,
> >     which I
> >     > haven't. I have only a series of dicom files or the .mri file
> >     generated by
> >     > ctf software from them. Can I still move on?
> >
> >     you need to do the coregistration and get a -trans.fif file.
> >
> >     A
> >     _______________________________________________
> >     Mne_analysis mailing list
> >     Mne_analysis at nmr.mgh.harvard.edu
> >     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> >     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> >     The information in this e-mail is intended only for the person to
> >     whom it is
> >     addressed. If you believe this e-mail was sent to you in error and
> >     the e-mail
> >     contains patient information, please contact the Partners Compliance
> >     HelpLine at
> >     http://www.partners.org/complianceline . If the e-mail was sent to
> >     you in error
> >     but does not contain patient information, please contact the sender
> >     and properly
> >     dispose of the e-mail.
> >
> >
> >
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140328/16ab452e/attachment.html