[Mne_analysis] a junior question on mne_setup_source_space
peng
prion.w at gmail.com
Fri Mar 28 11:40:32 EDT 2014
Thanks, dgw and junpeng for your feedback. I did read the manual before
asking:)
I am sorry '-src.fif' was a typo, I wanted to read -trans.fif. I did not
find a proper function in the manual.
To write it, <fiff_write_coord_trans> seem to be the correct function.
According to the manual, I set
==
t.from = 4 %(head);
t.to = 5 %(mri);
t.trans = M; %(4x4 matrix).
x = fopen('t.fif', 'w');
fiff_write_coord_trans(x, t);
fclose(x);
==
No complains from matlab in writing.
But mne_analyze complain that the file "does not start properly"...
On Fri, Mar 28, 2014 at 3:10 PM, dgw <dgwakeman at gmail.com> wrote:
> Hi Peng,
>
> The matlab toolbox chapter in the manual specifies how you read each
> file type. The function to read a "-src.fif" file is
> mne_read_source_spaces.
>
> D
>
> On Fri, Mar 28, 2014 at 9:14 AM, peng <prion.w at gmail.com> wrote:
> > 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
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