[Mne_analysis] mne_forward_solution results

Krieger, Donald N. kriegerd at upmc.edu
Wed Jan 20 13:22:27 EST 2010
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I think the problem is that numbers are actually there but mne_show_fif doesn't show them.  I think I have to convert the forward solution file to a matlab file and then access the forward solution matrix using matlab.  Perhaps you or someone else on the list can confirm this.

Don
 
Don Krieger, Ph.D., D.ABNM
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654


-----Original Message-----
From: Daniel G. Wakeman [mailto:dgwakeman at gmail.com] 
Sent: Wednesday, January 20, 2010 1:19 PM
To: Krieger, Donald N.
Cc: mne_analysis at nmr.mgh.harvard.edu
Subject: Re: [Mne_analysis] mne_forward_solution results

Hi Don,

Well, you may want to try to do this with an actual MRI instead of  
just using the surfaces from fsaverage. There are some dependencies  
upon having an actual MRI (which there isn't for fsaverage). I would  
try on a real MRI.

Dan
On 20 Jan 2010, at 17:43, Krieger, Donald N. wrote:

> Hi Dan,
>
> Thank you again for responding.  I very much appreciate it.
>
> I generated the source space using mne_volumne_source_space.  That  
> part appears to be OK since mne_list_source_space applied to the  
> results yields back the right answer.
>
> I haven't been able to get mne_do_forward_solution to work.  It  
> gives the error message: "Could not find the MRI data  
> directory ..."  But it appears that "do_forward_" is a wrapper  
> around "forward_" which does some automatic file naming.
>
> I'm not trying to get to an inverse solution at this point.  I just  
> want the forward solution values at the MEG sensors, given specific  
> dipole locations and orientations.
>
> Thanks again.
>
> Don
>
> -----Original Message-----
> From: Daniel G. Wakeman [mailto:dgwakeman at gmail.com]
> Sent: Wednesday, January 20, 2010 12:30 PM
> To: Krieger, Donald N.
> Cc: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] mne_forward_solution results
>
>
> Well, I don't really understand what the problem is (but I imagine
> someone will have the real answer). My two thoughts are that either
> there is a problem with the tags you included in mne_forward_solution
> (mne_do_forward_solution is designed to avoid the complexities of
> these commands), or whatever procedure you used to generate this
> source space may be not interpretable by mne_forward_solution. An
> alternative which would work, would be to generate a "grid source
> space" then to do the inverse solution by removing the uninteresting
> dipoles from the forward model and calculate the inverse solution in
> Matlab.
>
> D
> On 20 Jan 2010, at 17:06, Krieger, Donald N. wrote:
>
>> Hi Dan,
>>
>> Thanks for responding.  Yes, the two points are intentional.
>>
>> Here's a dump of where the dipoles are made using
>> mne_list_source_space:
>>
>> # CoordinateSystem "Head"
>> # begin   end  X (mm)  Y (mm)  Z (mm) Q(nAm) Qx(nAm) Qy(nAm) Qz
>> (nAm)    g/%
>>       1     1    30.0    50.0    80.0   10.0    2.67    5.35
>> 8.02  100.0
>>       2     2    40.0    40.0    70.0   10.0    5.96    2.98
>> 7.45  100.0
>> ## Name "ALL dipoles" Style "Dipoles2"
>>
>> If  there's a problem upstream, is there something in the output
>> from mne_forward_solution which indicates where it is?  The only
>> thing I see which might be that is:
>>
>> " Setting up compensation data...
>>           No compensation set. Nothing more to do."
>>
>> What do you think?
>>
>> Don
>>
>> -----Original Message-----
>> From: Daniel G. Wakeman [mailto:dgwakeman at gmail.com]
>> Sent: Wednesday, January 20, 2010 11:57 AM
>> To: Krieger, Donald N.
>> Cc: mne_analysis at nmr.mgh.harvard.edu
>> Subject: Re: [Mne_analysis] mne_forward_solution results
>>
>> Hi Don,
>>
>> Well, the first thing I noticed, is there are only two points in your
>> source space. Usually, this is quite odd. Is this intentional? The
>> problem may be further upstream.
>>
>> Dan
>> On 20 Jan 2010, at 16:51, Krieger, Donald N. wrote:
>>
>>> Dear List:
>>>
>>> I used mne_forward_solution per the messages written which are
>>> listed below my signature.  When I look in the output file,
>>> TestFwd.fif using mne_show_fiff I find no results.  The output from
>>> that is shown at the bottom of this message.  I truncated a couple
>>> of things but left what was before and after them to show that they
>>> do not include the forward solution results.
>>>
>>> Any thoughts or suggestion would be most appreciated.  Thanks.
>>>
>>> Don
>>>
>>> Don Krieger, Ph.D., D.ABNM
>>> Department of Neurological Surgery
>>> University of Pittsburgh
>>> (412)648-9654
>>>
>>> ==================================================================== 
>>> =
>>> =
>>> ======
>>>     MESSAGES PRINTED BY mne_forward_solution:
>>> Source space                 : fsaverages/TestSrc.fif
>>> MRI -> head transform source : fsaverages/fsaverage-trans.txt
>>> Measurement data             : ../../../MegData/
>>> 30Nov2009Sub103/30Nov2009Sub103Sess3_raw.fif
>>> Sphere model                 : origin at (   0.00    0.00    
>>> 40.00) mm
>>> Accurate field computations
>>> Do computations in head coordinates.
>>> Free source orientations
>>> Destination for the solution : TestFwd.fif
>>>
>>> Reading fsaverages/TestSrc.fif...
>>> Read 1 source spaces a total of 2 active source locations
>>>
>>> Coordinate transformation: MRI (surface RAS) -> head
>>>          0.999990  0.003550  0.000200     -1.76 mm
>>>         -0.003560  0.998390  0.056630     31.10 mm
>>>         -0.000000 -0.056630  0.998400     39.59 mm
>>>          0.000000  0.000000  0.000000     1.00
>>>
>>> Read 306 MEG channels from ../../../MegData/
>>> 30Nov2009Sub103/30Nov2009Sub103Sess3_raw.fif
>>> Coordinate transformation: MEG device -> head
>>>          0.999638 -0.025515 -0.008600     -3.00 mm
>>>          0.026165  0.995902  0.086571      6.55 mm
>>>          0.006356 -0.086765  0.996209     43.93 mm
>>>          0.000000  0.000000  0.000000     1.00
>>> EEG not requested. EEG channels omitted.
>>> 54 coil definitions read
>>> Head coordinate coil definitions created.
>>> Source spaces are now in head coordinates.
>>> Using the sphere model.
>>>
>>> Setting up compensation data...
>>>         No compensation set. Nothing more to do.
>>> Computing MEG at 2 source locations (free orientations, no
>>> threads)...done.
>>>
>>> writing TestFwd.fif...done
>>>
>>> Finished.
>>> ==================================================================== 
>>> =
>>> =
>>> ==================================================================== 
>>> =
>>> =
>>> ============
>>>      OUTPUT FROM THE FORWARD SOLUTION .fif FILE
>>> 100 = file ID                  1.2 0x123f5741810000 Wed Jan 20
>>> 11:29:38 2010
>>>  101 = dir pointer              -1
>>>  106 = free list                -1
>>>  104 = {                        350 = MNE
>>>  104 = {                        358 = MNE env
>>>  103 = block ID                 1.2 0x123f5741810000 Wed Jan 20
>>> 11:29:38 2010
>>> 3550 = MNE env wd               /home/kriegerd/MegShells/VEE/
>>> SrcSpaceFiles
>>> 3551 = MNE env command          mne_forward_solution --src
>>> fsaverages/TestSrc.fif --accurate --meg --meas ../../../MegDa
>>> ta/30Nov2009Sub103/30Nov2009Sub103Sess3_raw.fif --trans fsaverages/
>>> fsaverage-trans.txt --fwd TestFwd.fif
>>>  105 = }                        358 = MNE env
>>>  104 = {                        353 = MNE parent MRI
>>>  222 = transform                MRI (surface RAS) -> head
>>>                                  0.99999  0.00355  0.00020    -1.76
>>>                                 -0.00356  0.99839  0.05663    31.10
>>>                                 -0.00000 -0.05663  0.99840    39.59
>>>                                  0.00000  0.00000  0.00000     1.00
>>>  105 = }                        353 = MNE parent MRI
>>>  104 = {                        354 = MNE parent MEG
>>> 3508 = MNE file name            ../../../MegData/
>>> 30Nov2009Sub103/30Nov2009Sub103Sess3_raw.fif
>>>  222 = transform                MEG device -> head
>>>                                  0.99964 -0.02552 -0.00860    -3.00
>>>                                  0.02616  0.99590  0.08657     6.55
>>>                                  0.00636 -0.08676  0.99621    43.93
>>>                                  0.00000  0.00000  0.00000     1.00
>>>  200 = nchan                    306
>>>  203 = channel                    1 (113)       (MEG0113 [1]) T/m
>>> range: 1.90735e-05 cal: 3.25e-09
>>>  203 = channel                    2 (112)       (MEG0112 [1]) T/
>>> m       range: 1.90735e-05 cal: 3.25e-09
>>> 	<snip>
>>>  203 = channel                  305 (2643)      (MEG2643 [1]) T/
>>> m       range: 1.90735e-05 cal: -3.25e-09
>>>  203 = channel                  306 (2641)      (MEG2641 [1]) T
>>> range: 1.90735e-05 cal: 4.14e-11
>>>  105 = }                        354 = MNE parent MEG
>>>  104 = {                        351 = MNE src space
>>> 3518 = MNE src space type       3
>>> 3506 = MNE coordf               5
>>> 3512 = MNE src npoints          2
>>> 3510 = MNE src loc              2: 2 x 3 (float) [dense]
>>> 3511 = MNE src norm             2: 2 x 3 (float) [dense]
>>> 3513 = MNE src sel              2 ints
>>> 3514 = MNE src nuse             2
>>>  105 = }                        351 = MNE src space
>>>  104 = {                        352 = MNE fwd sol
>>> 3522 = MNE methods              1
>>> 3506 = MNE coordf               4
>>> 3521 = MNE src ori              2
>>> 3512 = MNE src npoints          2
>>>  200 = nchan                    306
>>>  104 = {                        357 = MNE named mat
>>> 3504 = MNE nrow                 6
>>> 3505 = MNE ncol                 306
>>> 3503 = MNE col names            MEG0113:MEG0112:MEG0 ....... <snip>
>>> 3520 = MNE fwd sol              2: 6 x 306 (float) [dense]
>>>  105 = }                        357 = MNE named mat
>>>  105 = }                        352 = MNE fwd sol
>>>  105 = }                        350 = MNE
>>>  108 = NOP
>>> ==================================================================== 
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>>> ====================================
>>>
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>>> Mne_analysis at nmr.mgh.harvard.edu
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>>
>
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