Hi,
On 18 Jul 2007, at 03:54, Vinod Venkatraman wrote:
> 1. Is calculating percent signal change for a [masked] ROI merely
> averaging
> the cope (or pe) values for all voxels in the mask (multiplied by the
> formula on the featquery page)? Or does it recompute the parameter
> estimates from the mean raw time series of in the masked region?
The PE/COPE is turned into a % change image _before_ any averaging is
done.
> 2. Is the max_pe1_ts.txt the time series for the voxel with highest
> percent
> signal change for the first PE in the mask? And the reason why this
> time
> series could be different for pe2 (max_pe2_ts.txt) is because a
> different
> voxel within the same mask has a higher value for the second PE?
Indeed.
> 3. What is in the mean_mask_ts.txt? Is this the average of the
> voxels in
> the mean functional image that is used in percent signal change
> calculation?
It is the average of the data in filtered_func_data over the ROI mask.
> 4. Based on earlier posts on this topic, what does it mean to
> choose zstat
> or tstat images as inputs for featquery? Does the output of
> featquery on
> these images give a sense of whether the corresponding contrast in the
> selected ROI is significant for each of the subjects queried on?
Indeed.
> 5. Finally, the voxel coordinates in standard space have decimal
> places.
> Why is this so? Is this because my outputs from first level are not
> in the
> standard space and my mask is in standard space. Should I convert my
> outputs from first level to standard space before running feat query?
The voxel coords in native FMRI space will be integer voxel coords.
The standard space mm coords will not in general be integers as a
general affine transformation is applied to get the voxel coord into
standard space. If you want to round to the nearest mm that's fine.
You don't need to convert your data to standard space - featquery
takes care of this transformation for you.
Cheers, Steve.
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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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