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> 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 = 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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