Re: [Freesurfer] problem with tksurfer

Yes, just add --trgsubject fsaverage doug

On 09/15/2012 07:02 PM, Maryam Vaziri Pashkam wrote:

Hi Doug,

This is a separate question but related to the volume to surface conversion. Is it possible to sample the sig.nii.gz file to the fsaverage surface instead of the individual subject surfaces using the mri_vol2surf? How should I change the command bellow to do that? I want to be able to load data from different subjects to a common space and see each subject's data as a different overlay on the same common space. Is that possible in freesurfer?

Thanks, Maryam

On Tue, Sep 11, 2012 at 11:06 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Maryam, I finally figured out what is going on. The bottom line
is that it is just a weird coincidence. The volume size is
70*70*33=161700 which happens to be exactly how many vertices are
in the left hemisphere of this subject. When tksurfer sees this,
it thinks that each voxel must be a vertex and displays it as such
instead of sampling the volume onto surface which is why it looks
so strange. There is not a way to force tksurfer to treat the
overlay as a volume, but instead (and probably better), you can
sample the volume onto the surface, then load it as an overlay, eg

mri_vol2surf --reg register.dof6.dat --hemi lh --mov sig.nii.gz
--o lh.sig.mgh --projfrac 0.5
tksurfer teal_tiger_kcb lh inflated -curv -overlay lh.sig.mgh

and the same thing with the right side.

The chances that this kind of thing happens must be several
million to one!
doug




On 09/06/2012 05:26 PM, Maryam Vaziri Pashkam wrote:

    Hi Doug,

    I uploaded the tar file. It is called incorrect_lh_test.tar

    Thanks,
    Maryam

    On Wed, Sep 5, 2012 at 10:04 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:

        Can you upload a tarball of the subject and the sig.nii.gz
    to our
        file drop?

    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>


        doug



        On 08/28/2012 10:18 AM, Maryam Vaziri Pashkam wrote:

            Hi Doug,

            Any other insight how I can solve this problem?

            Maryam

            On Fri, Aug 24, 2012 at 7:17 PM, Maryam Vaziri Pashkam
    <mvaziri@fas.harvard.edu <mailto:mvaziri@fas.harvard.edu>
    <mailto:mvaziri@fas.harvard.edu <mailto:mvaziri@fas.harvard.edu>>
    <mailto:mvaziri@fas.harvard.edu <mailto:mvaziri@fas.harvard.edu>

    <mailto:mvaziri@fas.harvard.edu
    <mailto:mvaziri@fas.harvard.edu>>>> wrote:

                It looks fine to me. I have attached the tiff
    image of a
            coronal
                slice. So this means that the registration of the
    surface
            to the
                anatomical is fine. This is strange. I tried the
    tksurfer
            with the
                original surface and the overlay on the rh looks
    fine and
            the left
                hemisphere has the same problem as on the inflated
            surface. Any
                other idea?

                M


                On Fri, Aug 24, 2012 at 6:54 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:


                    I don't understand your last paragraph. Does
    the lh
            surface
                    look ok, eg, when you run

                    tkmedit teal_tiger_kcb orig.mgz -surfs

                    doug




                    On 08/24/2012 06:37 PM, Maryam Vaziri Pashkam
    wrote:

                        Yes I have checked it multiple times. They
    are the
            same.
                        Here are the two lines:

                        tksurfer teal_tiger_kcb rh inflated -curv
     -overlay

     /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz
                         -overlay-reg

     /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat
                        -scalebarflag 1

                        tksurfer teal_tiger_kcb lh inflated -curv
     -overlay

     /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz
                         -overlay-reg

     /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat
                        -scalebarflag 1

                        I have copy pasted the inflated anatomical
    folder
            of the
                        subject from another computer. Is it
    possible that
            some
                        specific files are not copied properly? I dont
            know where
                        are the files that have the information for
            registration
                        of the anatomical brain to the inflated
    suface. My
            guess
                        is that is where the problem is. What do
    you think?


                        Maryam



                        On Fri, Aug 24, 2012 at 6:19 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>>
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    <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:


                            Hi Maryam, it seems very strange that one
            hemisphere
                        looks ok but
                            other looks bad. In fact, I'd say that
    it cannot
                        happen. The
                            differences are not likely to be due to
            version. Can
                        you double
                            check that the tksurfer commands for
    the lh
            and rh are
                        the same
                            (except for lh and rh, of course)
                            doug




                            On 08/22/2012 09:13 PM, Maryam Vaziri
    Pashkam
            wrote:

                                Hi Doug,

                                I am having a problem with
    tksurfer overlay
                        function. I ran
                                one analysis in freesurfer 5.1 on
    a mac
            machine
                        and I cannot
                                properly load it on the surface. The
            analysis was
                        performed in
                                the native space. When I use
    tksurfer to
            load the
                        analysis on
                                the surface using the overlay
    function I
            dont get
                        an error but
                                the output image just shows small
    dots on the
                        surface instead
                                of patches of activity. It looks
    like the
                        registration is not
                                correct. I checked the
    registration on the
            volume
                        and it looks
                                fine to me. This only happens with
    one of my
                        subject and only
                                on his left hemisphere. I have
    attached
            two tif
                        images called
                                lhnative.tif and rhnative.tif that
    show the
                        results. I also
                                ran the analysis on the surface
    for both
            left and
                        right
                                hemisphere, and it looks fine
    (lhsurf.tif and
                        rhsurf.tif files
                                attached).
                                Any Idea how to solve this problem? My
            guess is
                        that the error
                                is in the registration of
    anatomical volume to
                        anatomical
                                surface in the left hemisphere of this
            specific
                        subject, but I
                                dont know how to solve this issue.

                                here is the code that I use to
    load the
            data on
                        the surface:

                                tksurfer teal_tiger_kcb lh
    inflated -curv
             -overlay

    /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz
                                 -overlay-reg

    /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat
                                -scalebarflag 1

                                Just a note that the recon-all was
            performed in
                        freesurfer 4.5
                                and the analysis on freesurfer
    5.1. Any chance
                        this might have
                                caused the error?

                                Thanks,
                                Maryam


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