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

Jeff Eriksen eriksenj at ohsu.edu
Tue Apr 17 20:55:34 EDT 2012
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Alex, Matti, et al.,

I placed a file in my DropBox:

http://dl.dropbox.com/u/74096906/MNE_Archive.zip

It has four files:
A1_smpl.edf
A1_smpl.fif
gsn257.elp
COR-xxxxxx.fif

Please see my last email regarding these. Thanks,
-Jeff


On 4/17/12 12:07 AM, "Alexandre Gramfort" <gramfort at nmr.mgh.harvard.edu>
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/AIRC00
>>>01-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/AIRC00
>>>01-5120-5120-5120-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/AIRC00
>>>01-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
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> --
>> 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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