Dear Chou-Ching,
2010/4/21 林宙晴 <[log in to unmask]>:
>
> Dear Vladimir
> Thanks again for the help.
> The data files are appended.
> By the way, there are some points (not really bugs) that if modified might
> be more convenient to use DCM-IR.
> 1. The bottom at left lower corner (Invert DCM). When hit, if you change
> mind and cancel it, it still shows estimating (in red), even though I think
> the process is stopped.
If by cancelling you mean pressing Ctrl-C, it'd be a little bit
difficult to change the colour of the button because you basically
interrupt the program and it doesn't do anything any more so also
doesn't do GUI updates. It can be done with trial/catch but I'd rather
leave the possibility for the program to crash normally because it's
more useful for debugging. I don't think the button is a big deal.
> 2. The bottom of Hanning filter is not functioning (can not be chosen).
This is correct GUI behaviour because the Hanning option is not
relevant for DCM-IR.
> 3. After the completion of estimation, the loaded DCM file is modified
> before the 'save' bottom is hit. It might be better to save to another file?
> because most of the time, the loaded DCM is used as a template.
What you should do is load your template, make the necessary changes
and then press 'Save' and change the name before you hit 'Estimate'.
> 4. Is it possible to restrict the search range of onset time, because
> sometimes you know the bound of onset time? However, DCM just searches the
> whole time range and find a solution outside the bound.
>
It's not possible to restrict the range, but it should be possible to
increase the prior precision of the onset parameter which will have
similar effect. However, looking at the code it's not immediately
obvious to me how to do it. I'll find out from Karl and get back to
you.
Vladimir
> Sincerely,
> Chou-Ching
>
> 2010/4/21 Vladimir Litvak <[log in to unmask]>
>>
>> Dear Chou-Ching,
>>
>> 2010/4/16 林宙晴 <[log in to unmask]>:
>> >
>> >
>> > Dear Vladimir
>> >
>> > Thank you very much for your help.
>> >
>> >
>> >
>> > I am wondering how DCM deals with local and global minimum. At different
>> > multiples of 64 runs, sometimes A Hz and B Hz look different.
>> >
>>
>> Yes, we encountered the problem of local maxima also here and we are
>> planning to improve the optimization scheme to deal with it better.
>> You should always make sure you get decent fits before you interpret
>> the parameters. From our experience if your optimization gets stuck in
>> a local maximum (in this case it usually converges after <30
>> iterations) you can restart the inversion and answer 'yes' to 'use
>> previous priors' and 'use previous posteriors'. Then the optimization
>> should find a better solution.
>>
>> >
>> >
>> > Does the old version of spm_dcm_ind_data.m presented wrong data?
>> >
>>
>> Yes, if you use ECDs the data that is computed is wrong in the old
>> version (this is a specific problem in DCM-IR so the users of other
>> DCMs shouldn't panic).
>>
>> > So my results using the old file might be wrong?
>> >
>> Yes.
>>
>> >
>> >
>> > The attached file is an example that I have obtained by using DCM.
>> >
>> > When I type DCM.B, it shows [4x4 double] [4x4 double], but I can’t see
>> > the
>> > values.
>> >
>> > When it is reloaded into DCM, dots of B just disappears.
>> >
>> >
>>
>> Could you also send me the data (mat and dat)? I can't load the DCM
>> properly without it. You can use yousendit.com if it's too big.
>>
>>
>>
>> Best,
>>
>> Vladimir
>>
>>
>> >
>> > It seems those A Hz and B Hz data are stored, so that they can be
>> > re-plotted
>> > when the result DCM file is re-loaded.
>> >
>>
>>
>>
>>
>> >
>> > Sincerely,
>> >
>> > Chou-Ching
>> >
>> >
>> >
>> >>
>> >> 寄件人: Vladimir Litvak <[log in to unmask]>
>> >> 日期: 2010年4月15日 下午05時48分23秒格林威治標準時間-04:00
>> >> 收件人: "Chou-Ching K. Lin" <[log in to unmask]>
>> >> 副本: [log in to unmask]
>> >> 標題: Re: [SPM] Problems with DCM for M/EEG
>> >>
>> >> Dear Chou-Ching,
>> >>
>> >> On Thu, Apr 15, 2010 at 2:50 PM, Chou-Ching K. Lin <[log in to unmask]>
>> >> wrote:
>> >>
>> >> Hi, Dear SPM friends, now I am probing and running DCM for M/EEG
>> >> (induced
>> >> response). I found some small problems.
>> >>
>> >> First, it stops at 64 rounds of calculation every time before
>> >> convergence.
>> >> Is there any way to change this magic number, 64?
>> >>
>> >> 64 iterations should be sufficient to get close to the optimum even
>> >> with no convergence but if you'd like to increase this number you can
>> >> only do it by changing the code (spm_nlsi_N around line 278).
>> >>
>> >> Also we recently found a bug in how the data for DCM-IR was prepared.
>> >> Put the attached function in toolbox\dcm_meeg to fix it.
>> >>
>> >> Second, when I reload the saved DCM file, all the parameters are
>> >> recovered, but those dots for B in the lower box are missing (every
>> >> time).
>> >>
>> >> This might be a GUI problem. I haven't seen it before. You can send me
>> >> one example DCM file and I'll check.
>> >>
>> >> Third, is there any way to examine the calculated parameters (A and B)?
>> >> When I open the DCM result file in Matlab command line, it shows it is
>> >> a
>> >> matrix or structure. But it does not give me the values.
>> >>
>> >> The values are in the structure. I suggest that you put a breakpoint
>> >> in spm_dcm_ind_results when you do the results display, find the
>> >> relevant part if the code and see how what you are interested in is
>> >> extracted from the structure. Some things are not actually stored but
>> >> are computed on the fly from things that are stored. If you are just
>> >> interested in coupling matrices in Hz you can export them as images
>> >> using the option in the 'Results' part.
>> >>
>> >> Best,
>> >>
>> >> Vladimir
>> >>
>> >>
>> >
>> >
>
>
|