Dear Burkhard,
The warning is normal and has to do with mesh vertices being too
close. We always get it. In fact I turned it off in Fieldtrip code
because I'm tired of being asked about it so you shouldn't be getting
it any more after the next SPM update. The reduction of number of
modes is probably because of lines around line 187 of spm_dcm_erp.
Basically if all the variance is explained with 8 modes it won't let
you have more than that.
Best,
Vladimir
On Tue, Jul 19, 2011 at 3:28 PM, Burkhard Maess <[log in to unmask]> wrote:
> Dear Vladimir,
>
> I have observed the the Nmodes were reduced from 14 down to 8 by the
> function spm_dcm_erp.
> I used the debug mode to stop my program just before and after the
> spm_dcm_erp function call.
> Is it true the the singular or badly scaled matrix refers to the projected
> data matrix? And may SPM decide
> to use less modes due to this?
>
> thanks a lot,
> Burkhard
>
> K>> DCM.options.Nmodes
>
> ans =
>
> 14
>
> K>>DCM = spm_dcm_erp(DCM);
> computing surface normals
> Warning: Matrix is close to singular or badly scaled.
> Results may be inaccurate. RCOND = 1.089108e-16.
>> In forward/private/meg_ini>getcoeffs at 111
> In forward/private/meg_ini at 53
> In ft_prepare_vol_sens at 275
> In spm_dcm_erp_dipfit at 139
> In spm_dcm_erp at 56
>
> K>> DCM.options.Nmodes
>
> ans =
>
> 8
>
>
>
> Vladimir Litvak wrote:
>>
>> Dear Burkhard,
>>
>> The number of modes is not exactly a filter for spatial frequency but
>> a number of PCA components to which your channel data is reduced prior
>> to fitting the model. It's actually slightly more complicated than
>> that but I won't go into the details. This number should be more than
>> the number of independent things you expect in the data so at least
>> the number of sources in your model, preferably plus a couple of extra
>> components. When you look at the 'channels' view of DCM results you
>> should see that high-numbered components don't contain any interesting
>> activity. If they do, perhaps you should add some more.
>>
>> Best,
>>
>> Vladimir
>>
>> On Mon, Jul 18, 2011 at 8:51 AM, Burkhard Maess <[log in to unmask]> wrote:
>>
>>>
>>> Hallo Vladimir,
>>>
>>> do you have recommendations how to choose this value?
>>> I understand that this is works as a spatial filter. Smaller number means
>>> smaller spatial frequency for the magnetic field distribution.
>>> Visualizations of the forward model and the filtered data would be great
>>> to
>>> see the impact of this filtering.
>>> Can you do this somehow?
>>>
>>> thank you very much for your help,
>>> Burkhard
>>>
>>>
>>>
>>>
>
> --
> ------------------------------------------------------------
> Dr. Burkhard Maess
> Max Planck Institute for Human Cognitive and Brain Sciences
> Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig
> Aussenstelle Bennewitz, phone/fax: +49(3425)887525-26/-11 mail: maess 'at'
> cbs.mpg.de, http://www.cbs.mpg.de
> ------------------------------------------------------------
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> preferred over .doc(x)
>
>
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