It will be the activation weighted by the windowing function, in this
case that 8ms Gaussian centered at your peak.
Vladimir
On Wed, Jul 20, 2011 at 11:11 PM, Urs Bachofner <[log in to unmask]> wrote:
> Hey Vladimir,
>
> haha, thanks, being a neuropsychology student myself I'm sure I understand
> this pretty clearly, the question was more regarding the output file...
> since there will be no time scale in the nifti file, will the output be an
> average activation of the 8ms time span?
>
> In your debt,
>
> Urs
>
>
> Am 21.07.2011 00:24, schrieb Vladimir Litvak:
>>
>> Dear Urs,
>>
>> This is a design decision of Karl who thought that physiological
>> features of ERP cannot be shorter than that. There is something called
>> 'matched filter theorem' that suggests that your time resolution
>> should match the extent of the features you are interested in. So
>> although you have very high sampling rate, the brain doesn't get any
>> faster because of that.
>>
>> Vladimir
>>
>> On Wed, Jul 20, 2011 at 10:53 PM, Urs Bachofner<[log in to unmask]>
>> wrote:
>>>
>>> Dear Vladimir,
>>>
>>> Thank you a lot for the dozenth time.
>>>
>>> Yes, since I know the exact milisecond of the peak I'm interested in I
>>> will
>>> rewrite all of my Nifti Images in the way you told me. (Thankfully this
>>> is a
>>> step after the Inversion so it will not take a lot of time)
>>>
>>> Thanks for clearing that up - still remains the question: If the time
>>> span
>>> of the Nifti images is non-existant, why is there an 8 ms time span
>>> there?
>>> Is it because I am spoiled to work with a sampling rate of 1000/s?
>>>
>>> Best,
>>>
>>> Urs
>>>
>>>
>>>
>>>
>>> Am 21.07.2011 00:05, schrieb Vladimir Litvak:
>>>>
>>>> Dear Urs,
>>>>
>>>> You are right, sorry. I meant the 'Window' button. If you specify the
>>>> same time point twice you'll get the shortest possible time window
>>>> which is Gaussian with FHWM of 8 ms. But usually activations are not
>>>> that short so perhaps you should define a longer window around your
>>>> peak of interest. Also note that if you want to compare several time
>>>> windows in your stats you should specify them all at once (separated
>>>> by semicolon).
>>>>
>>>> Best,
>>>>
>>>> Vladimir
>>>>
>>>> On Wed, Jul 20, 2011 at 10:36 PM, Urs Bachofner<[log in to unmask]>
>>>> wrote:
>>>>>
>>>>> Dear Vladimir,
>>>>>
>>>>> I think if I agree with you we'd both be wrong! :)
>>>>>
>>>>> I'm asked to specify the time span and frequency I'm interested in when
>>>>> pressing the "Window" button. When I press the "Image" button, I'm not
>>>>> asked
>>>>> to specify anything and it just writes the Nifti Image (and I updated
>>>>> to
>>>>> the
>>>>> newest versions some weeks ago).
>>>>> I'm lucky to know exactly where the peaks i'm interested in are since I
>>>>> use
>>>>> a matlab script that displays me the exact time point of the peak of my
>>>>> interest.
>>>>> So did I get you correctly that you advice me to enter that exact
>>>>> instant
>>>>> of
>>>>> time after pressing the "Window" button (and leave the frequency band
>>>>> of
>>>>> interest to zero, default) to get the Nifti image at the time point of
>>>>> interest?
>>>>> But then again, I think after pressing the Window button it clearly
>>>>> demands
>>>>> two time points, which I thought was the span of one trial.
>>>>>
>>>>> Looking forward to your answer!
>>>>>
>>>>> Thank you a lot, again,
>>>>>
>>>>> Urs
>>>>>
>>>>>
>>>>> Am 20.07.2011 23:20, schrieb Vladimir Litvak:
>>>>>>
>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
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>>>
>
>
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