[Mne_analysis] head coordinate transform not found
Jeff Eriksen
eriksenj at ohsu.edu
Tue Apr 17 19:36:37 EDT 2012
Matti,
I have tried again. I re-did the coordinate alignment using mne_analyse,
as follows:
***************************************************************************
********************
File:Load:Surface:inflated
File:Load:Digitizer Data:A1_smpl.fif -? loaded 260 points
View:ShowViewer -> loading additional surfaces, Viewer window appears with
scalp surface
ViewOptions:remove LR hemis, scalp transparent, show digitizer data ->
looks OK
Adjust:coordalign: mark LAP, Nas, RAP, align using fiducials
SaveMRI set -> COR-jefferiksen-120417-161409.fif (binary 16,859,028 bytes)
Savedefault -> A1_smpl-trans.fif (212 bytes)
Save -> A1_gsn257-trans.fif (212 bytes)
done-quite-exit
***************************************************************************
********************
For my own interest, I verified that all three trans files are binary, but
the COR- one definitely the larger by far.
So I tried to implicitly and explicitly use the COR- version, as follows:
***************************************************************************
*********************************
kje-macbook:MNE jefferiksen$ mne_do_forward_solution --bem
AIRC0001-5120-5120-5120-bem.fif --src AIRC0001-ico-3-src.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 : ./A1_smpl-trans.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
Coordinate transformation: MRI (surface RAS) -> head
0.999719 0.023663 -0.001043 -4.08 mm
-0.023374 0.992712 0.118220 1.13 mm
0.003833 -0.118163 0.992987 12.70 mm
0.000000 0.000000 0.000000 1.00
MEG -> head coordinate transformation not found.
Forward computation failed (see above)
kje-macbook:MNE jefferiksen$ mne_do_forward_solution --bem
AIRC0001-5120-5120-5120-bem.fif --src AIRC0001-ico-3-src.fif --meas
A1_smpl.fif --mindist 1.0 --eegonly --fwd A1_smpl_ico3-src.fif --mri
COR-jefferiksen-120417-161409.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 : COR-jefferiksen-120417-161409.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
Coordinate transformation: MRI (surface RAS) -> head
0.999719 0.023663 -0.001043 -4.08 mm
-0.023374 0.992712 0.118220 1.13 mm
0.003833 -0.118163 0.992987 12.70 mm
0.000000 0.000000 0.000000 1.00
MEG -> head coordinate transformation not found.
Forward computation failed (see above)
kje-macbook:MNE jefferiksen$
***************************************************************************
**********************
As you can see, both times I get "head coordinate trans not found".
Is there a step I have missed? I am sure it is something simple I am not
doing right.
Remember I am working purely with raw EEG data, unaveraged.
I am trying to understand where the information matching electrodes to BEM
scalp surface triangles or vertices is stored. I assume it is calculated
when I "Save MRI set"? Or is it not created until I use
mne_forward_solution? In any event, is there a way to visualize or list
the electrode locations after they have been projected onto the BEM scalp?
Thanks,
-Jeff
On 4/17/12 6:44 AM, "Matti Hamalainen" <msh at nmr.mgh.harvard.edu> wrote:
>
>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/AIRC
>>>>>0001-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/AIRC
>>>>>0001-5120-5120-5120-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/AIRC
>>>>>0001-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
>>>>
>>>>
>>>>
>>>>
>>>> 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
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> 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
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>
>
>_______________________________________________
>Mne_analysis mailing list
>Mne_analysis at nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
More information about the Mne_analysis
mailing list