2009/3/27 Lin Nga
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Hi all,
I have a few questions regarding the thresholding in FEAT:
1) I understand that with cluster thresholding, the voxels are first
thresholded by the Z threshold and then the resulting clusters are tested to
meet the Cluster P threshold.
What I want to know is, how do I find the p-value corresponding to the Z
threshold? Do I simply use the ztop (and ptoz for the reverse)? Just to
verify, this function calculates the p-value for that Z-score and NOT the
Cluster P threshold. Is that correct?
Yes. As you described, z-threshold and cluster-P are different parameters, for separate stages of the thresholding. ztop simply converts from the standardised z-statistic to the corresponding probablity that we obtained a statistic >= to this.
Also, if I'm conducting a whole brain analysis, I would want to use the #of
resels given at the bottom of the smoothness file under each COPE's stats
folder and not the resel count (# of resel/volume ?) for the ptoz function.
Am I misunderstanding this?
No, the number of resels is required only when you are selecting the option to calculate the z-stat associated with the GRF theory (this is relevant to the "voxel" thresholding option)
2) On a similar note but a different analysis, I have a set of localizer
data to find the FFA and I was hoping to get some advice on the threshold
settings. I am defining the FFA as a sphere (of 8mm radius) centered on the
most significantly activated voxel (within a certain range in the x,y,z
directions) from the contrast ( Faces - Items ). At the default settings for
the cluster thresholding ( Z threshold = 2.3 and Cluster P threshold =
0.05), I am only able to find FFAs in 31 out of the 47 participants. I was
hoping that I would be able to localize more FFAs with less stringent
thresholds.
I tried the no thresholding option under the Post-stats tab of FEAT but the
Post-stats report was blank except the the Post-stats title. Is this
supposed to happen?
You can find the non-thresholded images in the stats directory - zstat1.nii.gz etc.. Selecting "No thresholding" just tells FEAT not to run any thresholding.
I was considering Voxel thresholding but I need coordinates for the most
significant voxel; not sure how I would find it if it's not reported in the
results.
The voxel thresholding option in FEAT does not require a peak voxel coordinate - it is an alternate to cluster thresholding that determines a threshold based on GRF theory that is applied at every voxel (rather than clusters). If you do want to find the peak voxel, you can use fslstats function on the images in the stats directory.
In general, defining ROIs does not necessarily have to be based on whole brain thresholded maps - given the low SNR of fMRI, one would not always expect an ROI to be significant in every subject. People often use other methods to define subject localised ROIs, such as top 20% of voxels within a larger ROI.
Eugene
Since the FFA is a rather small area, I'm thinking that I should lower the Z
threshold and increase the Cluster P threshold but from previous posts, it
sounds like lowering the Z threshold below 2.0 isn't a good idea. I'm new to
GRF theory so I don't quiet understand why that is yet but from the ztop
function, a Z threshold of 1.65 corresponds to a p-value of 0.049471.
Doesn't that mean a Z threshold of 1.65 would still give me significant results?
Lastly, I am planning to re-run the post-stats with Z threshold=2.3 and
Cluster P threshold=1. Does that sound like a good idea? Does anyone have
any suggestions?
P=1? Do you mean P=.1? That should be OK.
Thanks in advance everyone!
Have a great weekend,
Lin
