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April 27, 2022 03:26PM
Howdy, Rookie-

This may be a bit of what you are doing already, but just to note:


When you run Clusterize in the GUI and open the Rpt (report), you can click "3dclust" in the new panel and get an equivalent 3dClusterize command to run on the command line (it used to be a 3dclust command, but that syntax is paaaainful and we updated it a while ago in the new program, but didn't change the button name because it was nice and short).

You can run that command and indeed, output the table to a text file:
3dClusterize ... > o.cluster_report.txt
... and then view the contents with, say:
cat o.cluster_report.txt
or, to ignore the commented part,
1dcat o.cluster_report.txt

The column of interest with the cluster peak (from 3dClusterize's help) should be this one:
Max Int      : Maximum Intensity value for the volume cluster
The table generally stores the peak Olay value, not Thr. We generally recommend visualizating the beta (= effect estimate or coefficient) from stat modeling, while using the stat as Thr. If you wanted the peak Thr for this, you could use the stat value as Olay, as well as for THr, and then the reported Max Int value would be the same value as your Thr.

The Max Int appears to be the 13th column (with one-based counting) in the table. You can print out the 13th column values with, say:
1dcat o.cluster_report.txt  | awk '{print $13}'

# or, redirecting to a file:
1dcat o.cluster_report.txt  | awk '{print $13}' > o.peak_thr_list.txt

Note in all of this, we often recommend looking at a lot more than just the statistic from FMRI datasets:
Is the statistic value all we should care about in neuroimaging?
https://pubmed.ncbi.nlm.nih.gov/27729277/
... and also there is more to clusters than just peaks:
Sources of Information Waste in Neuroimaging: Mishandling Structures, Thinking Dichotomously, and Over-Reducing Data
https://www.humanbrainmapping.org/files/Aperture/Accepted%20Works%20PDF/Chen_Sources_of_information_waste_in_neuroimaging.pdf
For example, looking at the what regions the clusters overlap might be useful.

Happy to discuss more about this.

--pt
Subject Author Posted

How to automate getting Peak t Cluster Values Attachments

Rookie April 27, 2022 01:52PM

Re: How to automate getting Peak t Cluster Values

ptaylor April 27, 2022 03:26PM

Re: How to automate getting Peak t Cluster Values Attachments

Rookie April 27, 2022 04:02PM

Re: How to automate getting Peak t Cluster Values

ptaylor April 27, 2022 05:55PM

Re: How to automate getting Peak t Cluster Values Attachments

Rookie April 28, 2022 04:24PM

Re: How to automate getting Peak t Cluster Values

Rookie April 30, 2022 12:55PM

Re: How to automate getting Peak t Cluster Values

ptaylor April 30, 2022 07:48PM



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