It is probably better to work with the y.mgh file that qdec produces. It is in fsaverage space. If you create an ocn file with mri_surfcluster, you can feed that as the --seg to mri_segstats (along with --i y.mgh), spec the output with --avgwf to get a matrix of nsubjects  by nclusters (make sure to also include --exludeid 0)


On 01/23/2017 08:00 PM, Katherine Damme wrote:

Thank you so much!

This got me to the stage of having separate labels for each significant cluster, but I would like to extract the values from each subject to look at the raw data.

Do I have to use mri_label2label to move the label into each individual's space?

Can I use aparcstats2table to get a table of the individual values of the label?
(It seems that this is set up for the segmentation data)

Thank you again!


On Mon, Jan 23, 2017 at 11:44 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    Try mri_surfcluster. Run it with --help to get usage. You can set the
    threshold with --fdr. Make sure to use the --mask option passing
    it the
    mask.mgh from the qdec  output


    On 01/22/2017 07:56 PM, Katherine Damme wrote:
    > Hello Everyone,
    >
    > Is there a way to extract the significant clusters as masks from
    > significant group comparisons using qdec?
    >
    > All I can seem to find is  mri_glmfit-sim which doesn't quite
    > replicate the QDEC FDR 0.05 output and doesn't seem to make anything
    > that I could extract as a label, or hand drawing an ROI.
    >
    > I am working with a longitudinal model of cortical thickness, and
    > would like to extract the average thickness of each significant
    > cluster to understand the change in thickness.
    >
    > Thank you.
    >
    > Kate Damme
    >
    >
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