Use example_func2standard.mat instead.
Is thresh_zstat1 a higher-level output? If so, it already is in some
standard space.
ta
christian
On Tuesday, Jun 24, 2003, at 19:46 Europe/London, Andy Myers wrote:
> ok so i have played about abit and now got some pretty blobs, but which
> files do i register to the standard brain now? so i can overlay onto
> standard in e.g.mricro i thought it would be
>
> flirt -in thresh_zstat1 -ref
> /home/andy/EBA/sp_160603/run1/sp_run1.feat/reg/standard -applyxfm -init
> /home/andy/EBA/sp_160603/run1/sp_run1.feat/reg/
> example_func2standard.xfm -ou
> tput_file
>
> but this doesnt seem to work, is it the example_func2stadard.xfm bit
> that
> needs replacing with another file?
>
> thanks
>
> andy
> ----- Original Message -----
> From: "Christian F. Beckmann" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Tuesday, June 24, 2003 5:49 PM
> Subject: Re: [FSL] Higher Level analysis and Mean's
>
>
>> Hi
>>
>> depends on the question you have: If it's the random effects question
>> then random effects analysis makes sense (and you potentially have to
>> live with an answer you might not like).
>> RFX not generating significant results could be for a variety of
>> reasons, you should try and interrogate your data further to see if
>> you
>> can find a reason for this (e.g. suboptimal first-level model,
>> inflated
>> first-level variance due to artefacts etc )
>>
>> If it's not RFX you're after then yes, use something else. If you're
>> happy with just asking about the effect within your sampled population
>> of subjects use simple fixed effects analysis.
>>
>> ta
>> christian
>>
>>
>>
>>
>>
>> On Tuesday, Jun 24, 2003, at 16:58 Europe/London, Andy Myers wrote:
>>
>>> do you think a different type of analysis would be more suitable?
>>>
>>> andy
>>>
>>> ----- Original Message -----
>>> From: "Christian F. Beckmann" <[log in to unmask]>
>>> To: <[log in to unmask]>
>>> Sent: Tuesday, June 24, 2003 3:53 PM
>>> Subject: Re: [FSL] Higher Level analysis and Mean's
>>>
>>>
>>>> Hi
>>>>
>>>> well, possible given that you're doing a random effects analysis.
>>>> Even
>>>> if most of these contain 'activation' at the single level that
>>>> doesn't
>>>> imply that the RFX group map will show significant voxels too.
>>>> WRT unthresholded maps: look in the BLAH.gfeat/copeX.feat/stats/
>>>> for
>>>> the unthresholded higher-level zstat maps for each of the copes
>>>>
>>>> ta
>>>> christian
>>>>
>>>>
>>>>
>>>> On Tuesday, Jun 24, 2003, at 11:36 Europe/London, Andy Myers wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I have got my 8 runs of data that the higher level analysis said
>>>>> there
>>>>> was
>>>>> no mean activation on, and looked at the same voxel in standard
>>>>> space
>>>>> across
>>>>> the runs and there is defintely activation in the same areas a
>>>>> large
>>>>> percentage of the time, so i cant work out why the higher level
>>>>> anaysis has
>>>>> absolutely no activation in it at all. am i feeding in the right
>>>>> cope?
>>>>> i
>>>>> give feat the 8 cope3 images from the feat stats directort, should
>>>>> i
>>>>> do
>>>>> anything to these first such as standardise them or something, or
>>>>> is
>>>>> there a
>>>>> problem with my thresholding levels, would that cause a conflict?
>>>>>
>>>>> also if i wanted to look at the unthresholded zstat image then what
>>>>> do
>>>>> i
>>>>> need to register it to in order to view it? i tried standard space
>>>>> like with
>>>>> the first level thresh_zstat images but that didnt work (using
>>>>> flirt
>>>>> -in
>>>>> etc....................................................)
>>>>>
>>>>> andy
>>>>
>>
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