Hi,
Right - so you want to combine a pre-defined mask with subject-level-
zstat-thresholding - so effectively two masks to use within Featquery
- so yes, that level of complexity isn't handled by the scripts - so
yes, your suggested approach looks perfect - should be easy enough to
script.
Cheers.
On 11 Mar 2009, at 15:36, Daniel Shaw wrote:
> I believe checking the "Threshold stats images as well as masking"
> button thresholds the stats/cope image from which the % signal
> change values are derived. This isn't what I need. I need to get the
> % signal change values from only those voxels whose z score exceeds
> a given threshold.
>
> I believe I have now worked around this, but in a very cumbersome
> way. I (1) registered the composite masks to the native space of
> each subject, (2) masked the stats/zstat image with the registered
> mask, (3) thresholded the masked stats/zstat image, (4) binarised
> the product to mask the stats/cope image, and then (5) Featquerying
> the masked cope image. If there is a pipeline/easier way I'd welcome
> any suggestions.
>
> Dan.
>
> On Mar 11, 2009, at 6:52 AM, Steve Smith wrote:
>
>> Hi,
>>
>> Yes - that's what the "Threshold stats images as well as masking"
>> button is for.......sorry it's so confusingly named ;-)
>>
>> Cheers.
>>
>>
>>
>> On 10 Mar 2009, at 14:01, Daniel Shaw wrote:
>>
>>> Hi,
>>>
>>> By combining functionally defined masks from three different
>>> groups (by taking the logical
>>> OR), I have constructed composite masks that I would now like to
>>> 'Featquery'.
>>>
>>> I see that is very straight forward to compute the overall %
>>> signal change or to count the
>>> number of voxels with z values exceeding a given threshold within
>>> these composite masks
>>> for each individual, but is it possible to combine both measures
>>> and calculate the mean %
>>> signal change in only those voxels within the composite mask that
>>> exceed a given z value
>>> threshold? This is necessary because the size of the composite
>>> masks makes for very low
>>> mean % signal change values (0.04, for example).
>>>
>>> Any ideas would be gratefully received.
>>>
>>> Dan.
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>
> Daniel Shaw M.Sc.
> PhD student
> Brain & Body Centre
> University of Nottingham
> University Park
> Nottingham
> NG7 2RD
>
>
>
>
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---------------------------------------------------------------------------
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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