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

[Alexandre Gramfort]

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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>
>
> --
> 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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