Thanks, junpeng, though I am not familiar with python.
Thanks, dgw, I will try your way, perhaps also with combination of <
fiff_write_coord_trans>.
The reason I don't use the GUI is that it did not work well in my
environment. For example, when I re-set the location of LAP by clicking, I
saw the coordinates changed (e.g. 10 mm), but not in the graphics, the
green label was still in the original location. Then I used the button to
move the fiducials, this time, Nasion, LAP and RAP always moved together,
although I only chose one... If I accepted this unsatisfied alignment,
later automatic alignment only made it worse. I am using the latest MNE
and freesurfer, in MacOS 10.9.2 on a macbook pro. Maybe there are some
dependency problems with the version of libraries...
So I plan to output a transform matrix generated by other software to
-trans.fif format, and then load it to visualize in mne_analyze. Modify it
outside if not appropriate (it is quite possible that different software
define XYZ in a different way.), then visualize in mne_analyze again. It
sound painful, but I don't have better solutions other than that.
On Fri, Mar 28, 2014 at 5:24 PM, dgw <dgwakeman at gmail.com> 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> 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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