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> 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>

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>>> 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>>> 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>>
    <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>
    <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>>>
                    Fax: 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>
                    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>




                    The information in this e-mail is intended
    only for
                the person to
                    whom it is
                    addressed. If you believe this e-mail was sent
    to you
                in error and
                    the e-mail
                    contains patient information, please contact
    the Partners
                    Compliance HelpLine at
    http://www.partners.org/complianceline . If the e-mail was
                sent to
                    you in error
                    but does not contain patient information, please
                contact the
                    sender and properly
                    dispose of the e-mail.



            --         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>




-- 
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>