[Mne_analysis] mne_forward_solution results
Krieger, Donald N.
kriegerd at upmc.edu
Wed Jan 20 12:06:12 EST 2010
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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