Re: [Freesurfer] (no subject)

If this is a surface based analysis, then you'll need to add --surface fsaverage rh doug

On 11/02/2012 11:34 AM, Ryan wrote:

Doug, I ran: mri-glmfit --glmdir rh.rmanova --y rh.thickness.sm25.mgh --fsgd fsgd doss --C training-effect.mtx

On Thu, Nov 1, 2012 at 7:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

On 11/01/2012 06:35 PM, Ryan wrote:

    Doug,
       Picture 4 shows the difference between the medial surface
    for this analysis and for another type of analysis (where I
    created my own matrix file) that completed normally. Is this
    normal? I have never looked at this surface for errors before,
    which is why I ask.

That is normal. Usually, the medial wall is masked out.

       Picture 5 shows the command you just requested I run, and
    all points across the cortical mantle look like this image -
    nothing seems to be at exactly the same level.

That looks normal. What is your mri_glmfit command-line? Not the
mri_glmfit-sim cmd line.



    On Thu, Nov 1, 2012 at 5:55 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>>> wrote:

        The mask looks ok to me (I did not notice anything strange
    around
        the CC). How do the sig maps look? Is there any data set
    in there
        that is odd? you can evaluate this with

        tksurfer fsaverage lh inflated -ov glmdir/mask.mgh
    -fminmax .5 1-t
        y.mgh

        this will bring up a "time" course where each point is an
    input.
        See if there are any inputs that are always 0 or some
    other outlier.

        doug


        On 11/01/2012 04:50 PM, Ryan wrote:

            Doug,

               I attached the tksurfer images that I get with your
            command, the area around the corpus callosum is oddly
    yellow.
            What caused this mask problem, and how can I fix it?
    Thanks.


            On Thu, Nov 1, 2012 at 2:55 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:

                The problem is that the fwhm is not-a-number
            (glmdir/fwhm.dat).
                Usually this means that there is something messed
    up with
            the mask
                (glmdir/mask.mgh). View the mask to see what is up
                tksurfer fsaverage lh inflated -ov glmdir/mask.mgh
            -fminmax .5 1
                doug


                On 11/01/2012 02:39 PM, Ryan wrote:

                    Doug,
                       Here are the files.


                    On Thu, Nov 1, 2012 at 2:00 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>>>
    <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
    <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:

                        Can you send the command line and attach
    the files?
                        thanks
                        doug


                        On 11/01/2012 01:11 PM, Ryan wrote:

                            Doug,
                               I tried running mri_glmfit-sim
    without the --bg
                    flag and it
                            finished in 10 minutes without any errors.
            This has never
                            happened before, so I highly suspect these
            results. Do you
                            know what could be wrong? In case you
    need it,
            the summary
                            file output and terminal output are
    attached.

                               -Ryan


                        --     Douglas N. Greve, Ph.D.
                        MGH-NMR Center
    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>>>
    <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
    <mailto:greve@nmr.mgh.harvard.edu>>>>
                        Phone Number: 617-724-2358
    <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>
    <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
    <tel:617-724-2358>>>
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    <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358>
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                        Fax: 617-726-7422 <tel:617-726-7422>
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    <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422>
    <tel:617-726-7422 <tel:617-726-7422>>

    <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>>>>


                        Bugs:
    surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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                        FileDrop:
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    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>




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                    --            -Ryan


                --     Douglas N. Greve, Ph.D.
                MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
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    <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>
                Phone Number: 617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>>
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                Bugs:
    surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
                FileDrop:
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>




            --            -Ryan


        --     Douglas N. Greve, Ph.D.
        MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
        Phone Number: 617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>>
        Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
    <tel:617-726-7422>>

        Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
        FileDrop:
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>




    -- 
       -Ryan


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

-- -Ryan