Aha. Pull up a lower-level directory and in come all the z-stat options.
Thank you very much!
Jim Porter
TRiCAM Lab Coordinator
Elliott Hall N437
612.624.3892
www.psych.umn.edu/research/tricam
Christian Beckmann wrote:
> Hi Jim,
>
> you can try and run featquery on the lower-level feat dirs (rather
> than the higher-level gfeat directory) using the ROI as a mask. You
> can do this easily for all the lower-level feat directory with a
> single featquery call - that way you'll automatically get the maximum
> Z stats and a lot of other info for each of the runs.
> cheers
> christian
>
>
>
> On 8 Jan 2007, at 18:31, 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.
>>>>
>>>>
>>>
>
> --
> Christian F. Beckmann
> Oxford University Centre for Functional
> Magnetic Resonance Imaging of the Brain,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
> Phone: +44(0)1865 222551 Fax: +44(0)1865 222717
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