Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

There should also be a .annot file there too

On 08/15/2013 02:40 PM, Garikoitz Lerma-Usabiaga wrote:

Sorry Doug, I don't understand, I just have the cluster.mgh file with the MonteCarlo simulation results, is an .mgh file with a big significant cluster (mc-z.abs.sig.cluster.mgh).

Is there a way to create a label for each of the significant clusters?

thanks again and sorry if the question is too trivial! Gari

On Thu, Aug 15, 2013 at 7:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Give it the annotation (.annot) file





On 08/15/2013 01:26 PM, Garikoitz Lerma-Usabiaga wrote:

    Thanks Doug!
    Could you give me an example please?  I cannot get it to work,
    with this command I get a zero label...

    mri_annotation2label --subject fsaverage --hemi lh
    --annotation lh.mc-z.abs.sig.cluster.mgh --labelbase
    lh.mc_mycluster

    thanks again!
    Gari



    On Thu, Aug 15, 2013 at 4:44 PM, Douglas Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:


        Hi Gari, you can use mri_annotation2label
        doug


        On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote:

            Hi list,
            we have a cluster that survived the Monte Carlo
        simulation for
            thickness, and we would like to obtain more data from
        that exact
            cluster (volume for example), is it possible to
        automatically
            create a label from that cluster?

            If I use mri_binarize or mri_cor2label is not working (I
            understand that the clusters are not stored as individual
            vertexes in the .mgh file but I don't know what the
        format is.

            Thanks in advance!
            Gari

            PD: I am on a VPN and tksurfer is not working for manually
            creating a label with the contour of the cluster.


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