One possibility is to run mri_segstats passing it the cluster
thresholded volume as a mask. That way mri_segstats will only report on
values that are both in a cluster and a segment. There's probably a way
to do the same thing from featquery, but I'm not as familiar with that
as I am my own programs:).
doug
James N. Porter wrote:
> 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.
>>>
>>>
>>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[log in to unmask]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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