Hi Steve,
Thanks, that's actually what I've been doing right now, I should have
thought about it before asking to the list, sorry...
Here is what I have for the 2nd level report.log, the 2nd level being a
cross-session averaging within the same subject (here subj n. 187):
> /usr/local/fsl/bin/avwmerge -t bg_image
> /mri_data/187/analyzed_data/run1/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run1/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run2/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run2/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run3/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run3/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run4/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run4/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run5/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run5/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run6/reg_standard/reg/highres
> /mri_data/187/analyzed_data/run6/reg_standard/reg/highres
So it seems to be averaging across 12 copies of the same high_res, twice
per run... I don't understand exactly why it's doing this, but so far, I
know that my bg_image at the 2nd level is my subject high_res.
At the 3rd level I have this:
> /usr/local/fsl/bin/avwmerge -t bg_image
> /mri_data/187/analyzed_data/187_cross_session_average.gfeat/cope1.feat/example_func
>
example_func at the second level being created, I believe, when
featregapply is run at the beginning of the 3rd level analysis. And it's
a high_res, right?
So it's actually taking the example_func from the first subject in the
list, even though the Post Stats option for the background image was set
to Mean Highres...
Any idea what could have gone wrong, if anything?
Thanks
Stephane
Steve Smith wrote:
> Hi, check in the report.log file in both (2nd and 3rd) higher-level
> .gfeat directories and find the avmerge command that creates the
> bg_image file - this should tell you what images were fed into bg_image.
>
> Cheers, Steve.
>
>
>
> On 12 Mar 2007, at 22:29, Stephane Jacobs wrote:
>
>> Hello everyone,
>>
>> I'd like to check what exactly is the example_func file within each
>> copeX.feat directory output by higher level analyses. When searching the
>> archives, I found that quote from Mark Woolrich:
>>
>> "In higher-level analyses example_func.* in the copeX.feat dirs is soft
>> linked to bg_image.* in the gfeat dir. The bg_image.* is the background
>> image specified by the user in the GUI for rendering purposes (goto
>> Post-stats tab on the Feat GUI).
>> By default it is the group mean structural brain warped into
>> standard space.
>> Other options are available."
>>
>>
>> That's what I expected, however I'm a bit surprised by how good and
>> clear my
>> bg_image looks at the output of a 3rd level analysis averaging across 20
>> subjects... The Post_Stats option in FEAT was indeed set to MEAN
>> HIGHRES, as
>> it is by default, but I wonder if there could be a way this file is
>> not what
>> it's supposed to be (e.g. an individual high-res...).
>>
>> I can definitely upload the file if necessary. Any comment would be
>> greatly
>> appreciated.
>>
>> All the best
>>
>> Stephane
>
>
> ---------------------------------------------------------------------------
>
> 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
> ---------------------------------------------------------------------------
>
>
>
|