[Mne_analysis] mne_forward_solution results
Krieger, Donald N.
kriegerd at upmc.edu
Wed Jan 20 12:43:18 EST 2010
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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