Re: [Freesurfer] mri_anatomical_stats segmentation fault

The label that you sent applies to fsaverage. If you want to use it on a different subject, you should map it to that subject with mri_label2label doug

On 05/28/2013 03:00 PM, Rob Tennyson wrote:

The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview.

Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at "nvertices" in our "lh.white" file.

On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

how did you create the label? If it has more vertices than the
subject has then something is very wrong. You don't always get
segfaults, you might just get garbage and never know it.
doug



On 05/28/2013 02:32 PM, Rob Tennyson wrote:

    Hi Doug,

    It appears that the subject I'm having the PHC issue with has
    fewer than 163798 vertices - it has 123249 vertices - however,
    it seems that all of our subjects have fewer vertices and I do
    not run into an error with any other subjects with this label.

    Also, I'm able to load the label onto my data in freeview
    without any issue. I'm having some problems opening my
    surfaces with tksurfer on my lab desktop, though. Should I
    upload the subjects in question so you can take a look?

    Thanks!
    Rob


    On Tue, May 28, 2013 at 10:06 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:

        Nothing looks like it is wrong with that label. Can you verify
        that the white surface has not been changed since the
    label was
        created? Check how many vertices the white surface has with
        mris_info. The PHC label references a vertex index as high as
        163798. If the white surface does not have that many
    veritices,
        then that could cause the problem.
        doug



        On 05/28/2013 10:33 AM, Rob Tennyson wrote:

            Hi Doug,

            Attached are the three labels I'm having an issue with
    (each
            with a different subject). These are built from areas
    that we
            found functional differences between a healthy control
    group
            and a MDD group. I was going to take a look at the
    anatomical
            stats to see if there are thickness or volume
    differences as well.

            I am also going to review the white surface soon as Bruce
            suggested.


            On Tue, May 28, 2013 at 9:26 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>>
            <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:

                Rob, can you send me your label?

                doug

                On 05/27/2013 01:00 PM, Rob Tennyson wrote:
                > Hi All,
                >
                > I'm running "mris_anatomical_stats" with a few
    manually
            defined
                > labels. For a few of my subjects, I am getting
    the error:
                > "Segmentation fault" on one of the labels.
    However, the
            other
                manually
                > defined labels process without any errors on
    these same
            subjects.
                >
                > For example, I am running "mri_anatomical_stats" on
            subject 33_bay6
                > with a manually defined ERC label, a manually
    defined
            PHC label,
                and a
                > manually defined medial frontal gyrus label. The
    only
            label that
                runs
                > an error for this subject is the PHC label. This PHC
            label runs
                > without any errors on the rest of my subjects.
                >
                > Here is what is displayed when running a label
    that fails:
                >
                > "> mris_anatomical_stats -f PHC.stats.04.txt -l
            lh.PHC_1.label -b
                > 33_bay6 lh
                > limiting computations to label lh.PHC_1.label.
                > reading volume
            /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz...
                > reading input surface
                >
    /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white...
                > reading input pial surface
                >
    /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial...
                > reading input white surface
                >
    /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white...
                > Segmentation fault"
                >
                > Does anyone know what may be causing the
    Segmentation
            fault and what
                > steps I should take to fix it?
                >
                > Thank you for your help!
                > Rob
                >
                >
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                --
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                MGH-NMR Center
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
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