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SPM  July 2011

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Subject:

Re: 3D Source Reconstruction

From:

Vladimir Litvak <[log in to unmask]>

Reply-To:

Vladimir Litvak <[log in to unmask]>

Date:

Wed, 20 Jul 2011 22:20:33 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (113 lines)

Dear Urs,

When you press the Image button you are asked to specify time and
frequency window and the MIP image that you see then is the summary
over that time and frequency window and it will correspond to the
exported image (if there are several conditions or time windows only
one will be shown, but all will be exported). There is another MIP
that you get just after the inversion or when you press the MIP button
without specifying time or coordinates. This MIP corresponds to the
time of maximal activation which may or may not be what you are
interested in. But this is just done to display something and you are
always asked to specify explicitly the parameters for image
generation.

Best,

Vladimir

On Wed, Jul 20, 2011 at 9:47 PM, Urs Bachofner <[log in to unmask]> wrote:
> Dear Vladimir,
>
> thank you very much for your patient answer.
>
> I will have a look at the sections you pointed me to tomorrow again.
> I had the feeling that by generating the Nifti Image the whole length of the
> Trials would be involved.  But basically did I understand you correctly
> that:
>
> - When I press the Image button to generate the Nifti Image, the MIP-picture
> should be already in the time span which I'm interested in (which is usually
> indeed the maximum activation in MY data)? So that the generated Nifti File
> shows the activation within the milisecond I'm interested in, so the
> dimension of time will be obsolete in the file?
>
> Thank you a lot again,
>
> Urs
>
>
> Am 20.07.2011 20:05, schrieb Vladimir Litvak:
>>
>> Dear Urs,
>>
>> You sound quite confused indeed. Perhaps you should take a look at the
>> SPM EEG paper again (http://www.hindawi.com/journals/cin/2011/852961/)
>> particularly the parts about sensor-level statistics (Section 3,
>> Figure 2) and section 4.6. "Convert to images" menu has to do with
>> sensor-level statistics and what you are trying to do is source-level.
>> Analyze (.img + .hdr) and NIFTI (.nii) formats are very similar and
>> are used interchangeably in SPM. Either can be used for statistics. It
>> so happens that the sensor-level images are created in Analyze format
>> and source-level images in NIFTI. So the bottom line is, use source
>> images such as the one you sent me for statistics. You don't need to
>> do anything else.
>>
>> Regarding the time dimension, SPM does not support statistics for more
>> than 3 dimensions so it would not be possible to further analyze
>> images with both 3D space in time. You can only do analysis on both
>> time and space only at the sensor level because scalp maps can be
>> reduced to 2D. So you must summarize the time and frequency dimensions
>> as explained in the paper. If you want to look at multiple time
>> windows you can generate multiple images at the same time, but the
>> time windows will be at least ~8ms.
>>
>> Best,
>>
>> Vladimir
>>
>> On Wed, Jul 20, 2011 at 1:23 PM, Urs Bachofner<[log in to unmask]>
>>  wrote:
>>>
>>> Hi Vladimir,
>>>
>>> sorry to bother you again with an amateur's question but I would
>>> appreciate
>>> it if you could point me into the right direction.
>>>
>>> I'm still working with my EEG Files (induced) that are now converted into
>>> Nifti Files (by clicking the Image button in the Source Reconstruction
>>> menu). However I now read that for statistics you should choose "Convert
>>> to
>>> Images" in the drop down menu and after I did this to the .mat file I
>>> didnt
>>> get one Nifti File but two files for every good trial, a .hdr and a .img.
>>>
>>> Which of the files (the .nii or the .hdr/.img pair) am I supposed to use
>>> for
>>> statistical analysis?
>>>
>>> If I should use the .hdr/.img files, how can I get SPM to produce one
>>> averaged pair (induced) instead a pair for all good trials?
>>>
>>> If I should use the .nii file: Why is there no time scale in the image as
>>> I
>>> display it? I have trials of 600ms and would like to see the activation
>>> in
>>> each time point?
>>>
>>> (There is one nifti Image in the attachment)
>>>
>>>
>>> Thanks a lot for every bit of help
>>>
>>> Urs
>>>
>>>
>>>
>>> --
>>> NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!
>>> Jetzt informieren: http://www.gmx.net/de/go/freephone
>
>

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