[Mne_analysis] problem with do_forward_solution: cannot read the coord transform

Tue Apr 17 09:44:49 EDT 2012

Please consult the manual section 3.11. The files read with the --trans option are text files which are not produced by MNE. This option is included mainly for backwards compatibility. Any fif file containing the head/MRI coordinate transformation is specified with the --mri option. Section 3.11. of the manual also describes how the transformation file is automatically looked up if neither --mri nor --trans is present.

- Matti

On Apr 17, 2012, at 9:37 AM, dgw wrote:

> I haven't been able to get it to work well on my data either, but I have 
> been too busy to track it down. If you want an immediate solution, just 
> save the MRI set and use the MRI instead of the trans information.
> 
> D
> 
> Alexandre Gramfort wrote:
>> hi Jeff,
>> 
>> that's weird. Can you put the files somewhere to give it a try? e.g. dropbox
>> 
>> Alex
>> 
>> On Tue, Apr 17, 2012 at 7:27 AM, Jeff Eriksen <eriksenj at ohsu.edu> wrote:
>>> The --trans option overrides any searching. I also tried the regular -trans file and the default stored in mri/sets, same problem.
>>> Thanks,
>>> -Jeff
>>> 
>>> ________________________________________
>>> From: Hari Bharadwaj [hari at nmr.mgh.harvard.edu]
>>> Sent: Monday, April 16, 2012 8:49 PM
>>> To: Jeff Eriksen
>>> Cc: mne_analysis at nmr.mgh.harvard.edu
>>> Subject: Re: [Mne_analysis] problem with do_forward_solution: cannot read      the coord transform
>>> 
>>> I think there are some issues with which directories
>>> mne_do_forward_solution looks for the specified trans file and it varies
>>> with how you call the --trans option and which MNE build you are using.
>>> I'm not sure what specifically is the issue here but I'd try the
>>> following:
>>> 
>>> Rename your trans file to end in -trans.fif (i.e no 2 at the end) and
>>> place it in the same directory as the --meas file and use --trans default.
>>> 
>>> All disclaimers apply :P
>>> 
>>> Regards,
>>> Hari
>>> 
>>> 
>>> On Mon, April 16, 2012 8:42 pm, Jeff Eriksen wrote:
>>>> I tried to use mne_do_forward_solution, below, but got a complaint about
>>>> my transform. A dump of the transform contents looks OK to me.
>>>> Suggestions?
>>>> Thanks,
>>>> -Jeff
>>>> 
>>>> ________________________________
>>>> 
>>>> kje-macbook:MNE jefferiksen$ mne_do_forward_solution --bem
>>>> AIRC0001-5120-5120-5120-bem.fif --src AIRC0001-ico-3-src.fif --trans
>>>> gsn257-trans2.fif --meas A1_smpl.fif --mindist 1.0 --eegonly --fwd
>>>> A1_smpl_ico3-src.fif
>>>> 
>>>> mne_forward_solution version 2.9 compiled at Dec 21 2009 19:50:45
>>>> 
>>>> Source space                 :
>>>> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/bem/AIRC0001-ico-3-src.fif
>>>> MRI -> head transform source : gsn257-trans2.fif
>>>> Measurement data             : A1_smpl.fif
>>>> BEM model                    :
>>>> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/bem/AIRC0001-5120-5120-5120-bem.fif
>>>> Accurate field computations
>>>> Do computations in head coordinates.
>>>> Free source orientations
>>>> Destination for the solution : A1_smpl_ico3-src.fif
>>>> 
>>>> Reading
>>>> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/bem/AIRC0001-ico-3-src.fif...
>>>> Read 2 source spaces a total of 1284 active source locations
>>>> 
>>>> Cannot read the coordinate transformation
>>>> Forward computation failed (see above)
>>>> 
>>>> kje-macbook:MNE jefferiksen$ mne_show_fiff --in gsn257-trans2.fif –verbose
>>>> 100 = file ID            1.3 0x304122003198 Mon Apr 16 17:10:33 2012
>>>> 101 = dir pointer     -1
>>>> 106 = free list         -1
>>>> 222 = transform      head -> MRI (surface RAS)
>>>>                                     0.99907 -0.01932 -0.03856     2.39
>>>>                                     0.00948  0.97056 -0.24066     0.03
>>>>                                     0.04207  0.24007  0.96984   -15.02
>>>>                                     0.00000  0.00000  0.00000     1.00
>>>> 108 = NOP
>>>> 
>>>> _______________________________________________
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>>>> Mne_analysis at nmr.mgh.harvard.edu
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>>> 
>>> --
>>> Hari Bharadwaj
>>> PhD Candidate, Biomedical Engineering,
>>> Boston University
>>> 677 Beacon St.,
>>> Boston, MA 02215
>>> 
>>> Martinos Center for Biomedical Imaging,
>>> Massachusetts General Hospital
>>> 149 Thirteenth Street,
>>> Charlestown, MA 02129
>>> 
>>> hari at nmr.mgh.harvard.edu
>>> Ph: 734-883-5954
>>> 
>>> 
>>> 
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