[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
Search archives:

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
>         >> >     _______________________________________________
>         >> >     Mne_analysis mailing list
>         >> >     Mne_analysis at nmr.mgh.harvard.edu
>         <mailto:Mne_analysis at nmr.mgh.harvard.edu>
>         >> >     <mailto:Mne_analysis at nmr.mgh.harvard.edu
>         <mailto:Mne_analysis at nmr.mgh.harvard.edu>>
>         >> >    
>         https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>         >> >
>         >> >
>         >> >     The information in this e-mail is intended only for the
>         person to
>         >> >     whom it is
>         >> >     addressed. If you believe this e-mail was sent to you
>         in error and
>         >> >     the e-mail
>         >> >     contains patient information, please contact the
>         Partners Compliance
>         >> >     HelpLine at
>         >> >     http://www.partners.org/complianceline . If the e-mail
>         was sent to
>         >> >     you in error
>         >> >     but does not contain patient information, please
>         contact the sender
>         >> >     and properly
>         >> >     dispose of the e-mail.
>         >> >
>         >> >
>         >> >
>         >> >
>         >> > _______________________________________________
>         >> > Mne_analysis mailing list
>         >> > Mne_analysis at nmr.mgh.harvard.edu
>         <mailto:Mne_analysis at nmr.mgh.harvard.edu>
>         >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>         >> >
>         >>
>         >> _______________________________________________
>         >> Mne_analysis mailing list
>         >> Mne_analysis at nmr.mgh.harvard.edu
>         <mailto:Mne_analysis at nmr.mgh.harvard.edu>
>         >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>         >
>         >
>         >
>         > _______________________________________________
>         > Mne_analysis mailing list
>         > Mne_analysis at nmr.mgh.harvard.edu
>         <mailto:Mne_analysis at nmr.mgh.harvard.edu>
>         > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>         >
>         >
>         > The information in this e-mail is intended only for the person
>         to whom it is
>         > addressed. If you believe this e-mail was sent to you in error
>         and the
>         > e-mail
>         > contains patient information, please contact the Partners
>         Compliance
>         > HelpLine at
>         > http://www.partners.org/complianceline . If the e-mail was
>         sent to you in
>         > error
>         > but does not contain patient information, please contact the
>         sender and
>         > properly
>         > dispose of the e-mail.
>         >
>         _______________________________________________
>         Mne_analysis mailing list
>         Mne_analysis at nmr.mgh.harvard.edu
>         <mailto:Mne_analysis at nmr.mgh.harvard.edu>
>         https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> 
> 
> 
>     _______________________________________________
>     Mne_analysis mailing list
>     Mne_analysis at nmr.mgh.harvard.edu
>     <mailto:Mne_analysis at nmr.mgh.harvard.edu>
>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> 
> 
>     The information in this e-mail is intended only for the person to
>     whom it is
>     addressed. If you believe this e-mail was sent to you in error and
>     the e-mail
>     contains patient information, please contact the Partners Compliance
>     HelpLine at
>     http://www.partners.org/complianceline . If the e-mail was sent to
>     you in error
>     but does not contain patient information, please contact the sender
>     and properly
>     dispose of the e-mail.
> 
> 
> 
> 
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> 


-- 
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



More information about the Mne_analysis mailing list