Re: [Freesurfer] Error when using --mask flag in mri_glmfit

The label will be totally off because it was not created in the conformed anatomical space of fsaverage. Does the mask look ok? If you want to view the label, use something like

tkmedit -f $SUBJECTS_DIR/fsaverage/mri.2mm/orig.mgz -ov sig.mgh -seg $SUBJECTS_DIR/fsaverage/mri.2mm/aseg.mgz

doug

On 11/19/2013 08:41 AM, Suzanne Oosterwijk wrote:

Hi Doug,

I use the following command to open tkmedit and then I load the mask, the ocn.mgh file or the original label (created by mri_binarize) as a segmentation (through the tkmedit menu). In this case a label does open, but it is totally off.

tkmedit fsaverage orig.mgz -aux brain.mgz -bc-main-fsavg -overlay /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol/omnibus/glm.amygdala/osgm/sig.mgh -fthresh 2.3 -fmax 4 -aparc+aseg

Thanks! Suzanne

On Thu, Nov 14, 2013 at 8:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

What is your tkmedit command used to view the segmentation?
doug


On 11/14/2013 07:10 AM, Suzanne Oosterwijk wrote:

    Hi Doug,

    Thanks for the code, this works. Nevertheless, I am a bit
    unsure about whether the masks that are used as input into
    this command are correct. I like to check all the stages of
    the process and when I open the mask.mgh file within the
    appropriate glm folder, the segmentation is totally off (the
    putamen is somewhere in the OFC). Furthermore, even though the
    file that holds the output cluster from the Monte Carlo
    simulation (mc-z.pos.23.lh.sig.cluster.mgh) seems correct, the
    segmentation file that I use as input into the mri_segstats
    command is also totally off (mc-z.pos.23.lh.sig.ocn.mgh) when
    I load it in tkmedit. Am I loading it incorrectly as a
    segmentation? Does this have anything to do with the fact that
    you advised me to use the 2mm version
    fsaverage/mri.2mm/aseg.mgz? Should I adapt for that in my
    tkmedit command?

    Finally, I also run into a problem with the nucleus accumbens
    specifically. For some reason I get an error when I run the
    glmfit and mc simulation within this specific mask. First I
    make the mask:

    mri_binarize --match 26 --i
    /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri.2mm/aseg.mgz
    --o
    /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/accumb_lh.mgz

    Then I run glmfit:

    set labels = (accumb)
    foreach label ($labels)
    mri_glmfit --y ces.nii.gz --osgm --glmdir glm.${label} --mask
    /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/${label}_lh.mgz
    mri_glmfit-sim --glmdir glm.${label} --sim mc-z 10000 2.3
    mc-z.pos.23.lh --sim-sign pos
    end

    But I get an error saying:

    FWHM = -nan
    ERROR: input FWHM is NaN (not a number).
      Check the mask in the glm directory.

    Any ideas what I am doing wrong?

    Thanks again!

    Suzanne


    On Tue, Nov 5, 2013 at 12:04 AM, Douglas N 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 Suzanne, there is probably an easier way to do this. If you
        create contrasts of each condition vs baseline then run
        isxconcat-sess on each, you can then run something like

        mri_segstats --seg mc-z.pos.23.lh.sig.ocn.mgh --i
        condition1.nii.gz --avgwf condition1.table.dat --excludeid 0

        where condition1.nii.gz is the output of isxconcat-sess for
        condition 1. The output fo mri_segstats will be
        condition1.table.dat which will have a row for each
    subject and a
        column for each of the clusters

        doug



        On 11/01/2013 09:51 AM, Suzanne Oosterwijk wrote:


            Hello again,

            I am stuck again in my analysis and I am not sure that
    my code
            is right. I want to do the following. With a Monte Carlo
            simulation I search for significant clusters within a
            particular ROI in my all conditions vs baseline
    contrast. Then
            I want to translate this functional cluster to each
            individuals native space (as a label) and extract percent
            signal change for each condition separately from that
    label.
            This is no problem in my surface analysis, but I am
    not sure
            how to do this in the volume. I ran the Monte Carlo
    simulation
            within the mask, which provides a segmentation called
            mc-z.pos.23.lh.sig.ocn.mgh. I assume that this would
    be the
            label that would go into mri_vol2vol to translate the
    cluster
            to native space. I found on the website, however, that you
            need to use tkregister first. So I used the following
    code,
            but I am doubtful about whether I am doing this right.

            tkregister2 --mov

    /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol
            /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --s
            ff_01_030512 --regheader --reg
    ff_01_030512/register.dat --surf

            The results of this command do not look good at
    all....(see
            attached image). The cluster in the -mov file does not
    overlap
            with the amygdala. For the next step, I assumed to use
            mri_vol2vol to save the cluster as a native space label,
            although I'd like to make sure the first step is correct
            before continuing with this step.

            mri_vol2vol --mov

    /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol

            /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh
    --reg
            ff_01_030512/register.dat --fstarg --interp nearest --o
            ff_01_030512/label/lh.amygdala.imact.mgz --s ff_01_030512


            What am I missing? Is the translation off because I did
            something wrong, or does that point to a deeper issue?


            Any help is much appreciated!


            Suzanne



            On Tue, Oct 29, 2013 at 6:04 PM, Douglas N Greve
            <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
            <mailto: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 suzanne, you'll need to use the 2mm version
                fsaverage/mri.2mm/aseg.mgz
                doug

                On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote:
                > Hello all,
                >
                > I want to run a Monte Carlo simulation within a
    volume
            ROI and I am
                > running into a problem when I use the --mask
    flag while
            running
                > glmfit. My question is very similar to the
    question asked in
                > "[Freesurfer] Volume-based Monte Carlo
    Restricted to a
            within mask
                > area" but I could not find the response to this
    question.
                >
                > Here is my code.
                >
                > First, I created a volume mask with mri_binarize:
                >
                > mri_binarize --match 18 --i
                >

     home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz
                > --o
                >

     /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
                >
                > I checked the mask and it looked good. Then I
    use the
            mask in
                glmfit.
                >
                > mri_glmfit --y ces.nii.gz --osgm --glmdir
            glm.amygdala_lh --mask
                >

     /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz
                >
                > When I do this, I get the following error:
                >
                > ERROR: dimension mismatch 1 between y and mask
                >
                > I guess this means that the ces.nii.gz file and mask
            file don't
                match,
                > but I have no idea how to solve this. Any thoughts?
                >
                > Thanks!
                > Suzanne
                >
                >
                > --
                >
                > Suzanne Oosterwijk, Ph.D.
                >
                > Postdoctoral Researcher
                >
                > Department of Social Psychology
                >
                > University of Amsterdam
                >
                > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu
    <mailto:s.oosterwijk@neu.edu>
            <mailto:s.oosterwijk@neu.edu
    <mailto:s.oosterwijk@neu.edu>>
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    <mailto:s.oosterwijk@neu.edu>>>>va.nl <http://va.nl>
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                >
                > https://sites.google.com/site/suzanneoosterwijk/
                >
                >
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            University of Amsterdam

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    <mailto:s.oosterwijk@neu.edu>
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    -- 

    Suzanne Oosterwijk, Ph.D.

    Postdoctoral Researcher

    Department of Social Psychology

    University of Amsterdam

    s.oosterwijk@u <mailto:s.oosterwijk@neu.edu
    <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> <http://va.nl>

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