Dear Antanas,
If you have no time then the best thing you can do is look by eye at
the PPMs and at activation movies, come up with some model or several
alternative models and test them with DCM.
I don't quite understand your problems with merged files but in
general when you have two conditions in the file and write out an
image, two images are written - one per condition and the numbers at
the end indicate which conditions it is so they are not overwriting
each other. See also the 'Sort conditions' functions that you can use
to make sure that the order of conditions is always the same (it'll be
the same anyway if you select the files in the same order for
merging).
The fastest and easiest thing to do is to merge all the conditions of
each subject in one file so you have one file per subject. You can put
each of those in a separate folder. Then press the 'Group inversion'
button and select all the files one by one. You will be able to
define a contrast (time window) and SPM will automatically write out
images for all the subjects. You can repeat this several times to get
different time windows but in this case the images will indeed have
the same name so you need to copy the previous ones into
subdirectories before repeating.
How to do statistical tests in SPM is a little too long a story for
one e-mail. It's basically what most of SPM is about. The starting
point is 'Specify 2nd level' button. It's quite easy to set up a
single sample t-test (default). You just need to select a group of
images and a directory for the output. But you'll have to look at the
manual (fMRI part) Chapter 10 and the example starting on page 274
about the contrast manager.
This might be a little too much to learn under time pressure, in that
case go back to my suggestion from the beginning. Keep in mind that
EEG has quite low spatial resolution (2-3 cm) so you don't need to be
very precise in the source locations you specify.
Hope this helps.
Vladimir
On Sat, Aug 15, 2009 at 8:52 PM, Spokas
Antanas<[log in to unmask]> wrote:
> Dear Vladimir,
>
> Thank you for response. I have tried to make do with multiple time windowed
> exported images, but it takes up a lot of time and is pretty crude, and I
> have no time left, unfortunately.
> In order to build contrasts, will again take too much time, as preprocessing
> has been done with another software, therefore all my subjects and
> conditions are in different files, so when I merge files as in CA1+EA1 in
> order to build after a contrast [1 -1], I can't do CA1+EA1, as it will be
> ovewritten on the first merged file, so that after every merge, I have to
> separately save it in different name, and I might finally get lost around
> files?
> I am afraid I don't know how to perform t-test on group of images, as they
> are saved in formats *.hdr, *.img, or are you talking about different kind
> of images? Thank you for your help,
>
> Regards,
> Antanas
>
> ________________________________
> From: Vladimir Litvak <[log in to unmask]>
> To: Spokas Antanas <[log in to unmask]>
> Cc: [log in to unmask]
> Sent: Saturday, 15 August, 2009 16:09:49
> Subject: Re: [SPM] eeg source reconstruction results
>
> Dear Antanas,
>
> I understand what you are trying to do, but in general I think it'd be
> hard to build a good DCM model just based in imaging source
> reconstruction without incorporating any prior knowledge from the
> literature and theoretical conciderations.
>
> If you have multiple subjects and conditions you should build SPMs for
> the contrasts of interest and look at the areas that come up in these
> contrasts. The next best thing would be to do just a single-sample
> t-test for a group of images from the same time period for different
> subjects. This is not valid statistical inference because all the
> values in the images are positive, but you can look at the peaks of
> the T-images as most consistently occurring sources.
>
> Finally the most ad hoc approach is to export images for the time
> periods of interest for single subjects and look where you find local
> maxima in those images.
>
> Best,
>
> Vladimir
>
> On Sat, Aug 15, 2009 at 3:48 PM, Spokas
> Antanas<[log in to unmask]> wrote:
>> Dear Vladimir,
>>
>> Thank you so much for your always prompt and helpful answers. Let me
>> explain, why I think I need more elaborate results, which I am not sure
>> how could be solved with contrast functions.
>> I am trying to get MNI coordinates for DCM. First I wanted to see what
>> solution could unrestricted imaging reconstruction give me according to my
>> experiment data and then restrict solutions by given in the literature and
>> compare if they would give me better evidence, if so, I could procede with
>> those coordinates and construct DCMs. As result output only gives most
>> active source coordinates at specified time point, it could be that
>> several
>> regions have the same time course of activation but with a slight
>> difference
>> in intensity, so that it won't show up at any time point, unless I procede
>> with window/image function, but then for any other active voxels I have no
>> info on their confidence levels. Is there something I could do with GUI? I
>> am sorry if this doesn't look clear, if not, I could try to elaborate.
>> Thank you again!
>>
>> Regards,
>> Antanas
>>
>> ________________________________
>> From: Vladimir Litvak <[log in to unmask]>
>> To: Spokas Antanas <[log in to unmask]>
>> Cc: [log in to unmask]
>> Sent: Saturday, 15 August, 2009 15:06:49
>> Subject: Re: [SPM] locations of stored ppm's and time courses of estimated
>> sources files after eeg imaging source reconstruction
>>
>> Dear Antanas,
>> Time course and PPMs are not stored but computed on the fly by the
>> function
>> spm_eeg_invert_display based on output of the inversion which is stored in
>> the header file. Using the GUI is the simplest way to access them. If you
>> want to do statistics on activations you should use the standard pathway
>> described in the manual.
>> Best,
>> Vladimir
>>
>> On 15 Aug 2009, at 14:55, Spokas Antanas wrote:
>>
>> Dear SPM,
>>
>> Could you please help me to locate files of stored ppm's and time courses
>> of
>> estimated sources after eeg imaging source reconstruction. Thank you very
>> much!
>>
>> Regards,
>> Antanas
>>
>>
>>
>>
>
>
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