Hello Doug-
Well, I suppose the problem is I'm unsure of the formula used to
calculate z-stats from intensity values. Since FEAT doesn't know what my
ROIs are, I assume that my N-size/population is all the voxels in the
brain, but is mu the mean value of all brain voxels, or does FEAT use
info from FAST to know when a voxel is labeled as grey or white matter
and use the appropriate mean greyscale value?
Basically, my issue is that when I run FEAT and take a look at, for
example, cluster_zstat1.html, then I get a great table of clusters and
voxel counts and max z-stats. However, these clusters are distributed
across the brain, and I want to know specifically what are the max
z-stats for each individual in a particular predefined cortical region.
Yes, the table includes xyz coordinates and I could locate each cluster
individually, but that's not a feasible option across dozens of subjects
with multiple analyses. So, in an attempt to streamline things I've run
reg-feat2anat and associated processes to create binary masks of
particular cortical regions, and hoped to obtain the same cluster list &
local maxima tables found in cluster_zstat1.html, but constrained by my
ROIs via masking in Featquery or pulling rows out of mri_segstats.
I suppose if I knew what FEAT was using as mu, sigma, and N, then I
could use the max intensity value output to calculate my own max z-scores.
Thanks for your assistance.
Jim Porter
TRiCAM Lab Coordinator
Elliott Hall N437
612.624.3892
www.psych.umn.edu/research/tricam
Doug Greve wrote:
> Hi James,
>
> mri_segstats will include the max for each segmentation. Is this not
> what you want? Or is it a format issue?
>
> doug
>
>
>
>
>
> On Sat, 6 Jan 2007, James Porter wrote:
>
>> Hello-
>>
>> I'm hoping to obtain outputs of activation z-statistics by ROI. I've
>> used
>> FreeSurfer to create ROI masks for all of my subjects, and run
>> Featquery to
>> obtain information about the ROI. However, I was disappointed to see the
>> output options do not give me the ability to generate tables of max
>> z-stats,
>> as the first-level FEAT output does.
>>
>> Likewise, I've used FreeSurfer's mri_segstats program to create stats
>> tables
>> delineated by ROI, but it gives similar output as Featquery.
>>
>> What path should I have gone down to obtain z-stat tables within masked
>> ROIs? My first thought right now is to run a first-level FEAT
>> analysis on
>> the masked functional volumes, but I'm willing to bet that you all
>> have a
>> better solution.
>>
>> Thanks for your help.
>>
>>
>
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