Hi Steve,
I am very worried that the negative PEs may be due to an error on my
part in the
way I modeled the experiment conditions in Feat. There were 18
conditions during
the experiment plus one condition for the fixation. I am only
interested in 6 of
the 18 conditions in the experiment, so I only had 6 EVs in my Feat
design plus
one EV for the fixation. I did not include the other conditions in the design.
Does this mean that my PE1 is the difference between EV1 and the conditions
that I did not include in the design file?
Should I add all the other conditions to the Feat model, and remove the
fixation
EV to solve this?
thanks,
Heather
Quoting Steve Smith <[log in to unmask]>:
> HI - maybe it just means that these images had no positive values
> within the mask?
> Cheers.
>
>
>
> On 13 Jul 2007, at 16:56, Heather Cogswell wrote:
>
>> Hi Steve,
>> Thank you for your prompt reply!
>>
>> I used the same binary mask for six contrasts on one subject. The
>> position of
>> the max voxel for some of the contrasts is (0 0 0 ) which does not
>> make sense.
>> I was wondering why this is happening? Below is a sample featquery with the
>> above problem (i.e. pe2 and pe4)
>>
>>
>> 1 stats/pe1 5 0.00 0.31 0.59 0.62 0.89 0.89 23 37 7 25.32 1.38 -15.90
>> 1 stats/pe2 5 -0.74 -0.74 -0.62 -0.70 -0.39 0.00 0 0 0 103.93
>> -112.31 -36.09
>> 1 stats/pe3 5 -0.35 -0.35 -0.07 -0.17 0.32 0.32 24 36 7 22.06 -1.59 -15.59
>> 1 stats/pe4 5 -2.54 -2.54 -1.94 -1.92 -1.46 0.00 0 0 0 103.93
>> -112.31 -36.09
>> 1 stats/pe5 5 -0.13 -0.13 0.52 0.59 0.90 0.90 24 36 7 22.06 -1.59 -15.59
>> 1 stats/pe6 5 -0.65 -0.65 -0.25 -0.45 0.64 0.64 24 37 7 22.03 1.34 -16.02
>>
>> Many thanks,
>> Heather
>>
>>
>>
>>
>> Quoting Steve Smith <[log in to unmask]>:
>>
>>> Hi,
>>>
>>> On 12 Jul 2007, at 16:30, Heather Cogswell wrote:
>>>
>>>> Dear FSL users,
>>>>
>>>> I'm an FSL newbie, so thanks in advance for your help!
>>>>
>>>> How can I make a mask from a 3rd level activation? I tried
>>>> avwroi but it
>>>> just creates the mask of the specific voxels that I input . . . I
>>>> want to
>>>> create a mask of the chosen voxels overlaid on the entire brain.
>>>
>>> I'm not sure what you're asking - you should probably take the
>>> appropriate thresh_zstat image from inside the appropriate
>>> something.gfeat/cope??.feat directory and maybe binarise this with
>>> avwmaths++
>>>
>>>> For Featquery analysis I can choose "stats/pe" or "stats/cope".
>>>> Which one
>>>> should I use for ROI analysis?
>>>
>>> It's up to you. If this isn't clear then you should probably read
>>> the FEAT manual carefully, including the intro to GLM etc stuff
>>> in it - hopfully then it will be clear which is what you want.
>>>
>>> Cheers, Steve.
>>>
>>>
>>>
>>>>
>>>>
>>>> Thanks,
>>>> Heather
>>>
>>>
>>> --------------------------------------------------------------------- ---
>>> ---
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Associate Director, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>> --------------------------------------------------------------------- ---
>>> ---
>>>
>
>
> ------------------------------------------------------------------------ ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ------------------------------------------------------------------------ ---
>
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