<div dir="ltr">Sorry, the last line should be <span style="font-family:arial,sans-serif;font-size:13px">read and write <*-<b>trans</b>.fif> file in matlab?</span></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Fri, Mar 28, 2014 at 2:14 PM, peng <span dir="ltr"><<a href="mailto:prion.w@gmail.com" target="_blank">prion.w@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Thank you Martin for the help.<div>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.</div>
<div>
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?</div>
<div><br></div>
</div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Mar 26, 2014 at 9:28 PM, Martin Luessi <span dir="ltr"><<a href="mailto:mluessi@nmr.mgh.harvard.edu" target="_blank">mluessi@nmr.mgh.harvard.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>On 03/26/14 16:00, peng wrote:<br>
> Thank you for the answers.<br>
> 1. Surprisingly I did not find any files were generated/saved after<br>
> running mne_setup_forward_model.<br>
<br>
</div>I assume there was an error, can you post the program output?<br>
<div><br>
> 2. I don't have a -trans.fif file. I tried to do it in GUI of<br>
> MNE_analyze, it was quite complicated. If I have a co-registered mri<br>
> file (generated by CTF software with .mri extension), can it be<br>
> converted to fif format? If not, I can read the 4x4 head2mri matrix via<br>
> matlab, can this information be written to fif format with certain tools<br>
> in MNE?<br>
<br>
</div>There is also a coreg GUI in MNE-Python, have a look here<br>
<br>
<a href="http://www.slideshare.net/mne-python/mnepython-coregistration" target="_blank">http://www.slideshare.net/mne-python/mnepython-coregistration</a><br>
<br>
You could write a .fif file with the transform in Matlab, but it seems<br>
to me that this wouldn't be easier than using the coregistration tools<br>
in mne_analyze or MNE-Python.<br>
<br>
HTH,<br>
<br>
Martin<br>
<div><br>
<br>
> Thanks again!<br>
><br>
><br>
> On Tue, Mar 25, 2014 at 11:39 PM, Alexandre Gramfort<br>
> <<a href="mailto:alexandre.gramfort@telecom-paristech.fr" target="_blank">alexandre.gramfort@telecom-paristech.fr</a><br>
</div><div>> <mailto:<a href="mailto:alexandre.gramfort@telecom-paristech.fr" target="_blank">alexandre.gramfort@telecom-paristech.fr</a>>> wrote:<br>
><br>
> hi,<br>
><br>
> > Some additional questions.<br>
> > 1 After I ran mne_setup_forward_model, I have no feedback from the<br>
> command<br>
> > line, is it normal?<br>
><br>
> it should print that it saved a file to disk<br>
><br>
> > 2 I am using CTF data, thus I converted the .ds folder from CTF to fif<br>
> > format with mne_ctf2fiff command, with option --infoonly. Here I<br>
> only want<br>
> > to get the Leadfield thus I suppose data is not necessary. However<br>
> when I<br>
> > try mne_do_forward_solution, it asked for mri description file,<br>
> which I<br>
> > haven't. I have only a series of dicom files or the .mri file<br>
> generated by<br>
> > ctf software from them. Can I still move on?<br>
><br>
> you need to do the coregistration and get a -trans.fif file.<br>
><br>
> A<br>
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