[Mne_analysis] a junior question on mne_setup_source_space
Martin Luessi
mluessi at nmr.mgh.harvard.edu
Fri Mar 28 13:24:58 EDT 2014
It should be straightforward to translate the function for writing
-trans.fif files from Python to Matlab. You can find the function here:
https://github.com/mne-tools/mne-python/blob/master/mne/transforms.py
HTH,
Martin
On 03/28/14 12:24, dgw wrote:
> presently in the matlab toolbox there is not a single function for
> reading a trans.fif file, but you can easily string together a couple of
> commands to do this. This should work on your file. I do recommend
> familiarizing yourself with the gui (using the sample data) as manually
> adjusting the transformation matrix in matlab is a highly risky business:
>
> [fid, tree, dir] = fiff_open('test-trans.fif')
> for t = 1:length(dir)
> if dir(t).kind == FIFF.FIFF_COORD_TRANS
> tag = fiff_read_tag(fid,dir(t).pos)
> break
> end
> end
> trans = tag.data
>
> Your code did not work, because your fid was not a fif fid (as described
> in fiff_write_coord_trans).
>
> HTH
> D
>
>
>
> On Fri, Mar 28, 2014 at 11:40 AM, peng <prion.w at gmail.com
> <mailto:prion.w at gmail.com>> wrote:
>
> 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 <http://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
> <mailto: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
> <mailto: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 <mailto: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>
> >> > <mailto: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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--
Martin Luessi, Ph.D.
Research Fellow
Department of Radiology
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School
149 13th Street
Charlestown, MA 02129
Fax: +1 617 726-7422
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