Re: [Freesurfer] Fwd: Problems dipslaying annotations in freeview

Did you select the right hemisphere when you load rh.annot? Whatever you do from the control panel on the left, it is applied to the selected layer, which is the one highlighted in the layer list.

Ruopeng

On 02/12/2014 01:16 PM, Laura Taylor wrote:

Hi Ruopeng and freesurfer folks,

I am still having trouble loading annotations in freeview, similar to what I mentioned before. When I load 'rh.aparc.a2009s.annot' in freeview, the annotation loads onto the LEFT hemisphere and is tye-died in appearance. In contrast, 'lh.aparc.a2009s.annot' loads correctly onto the left hemisphere and looks normal.

I have had this problem with many of my subjects. Can you help with this??

Thank you,

Laura

---------- Forwarded message ----------

Date: Thu, Jan 2, 2014 at 9:53 AM Subject: Fwd: [Freesurfer] Problems dipslaying annotations in freeview To: rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu

Hi Ruopeng,

I am forwarding the messages I sent to the freesurfer mailing list and that Doug suggested I ask you.

Basically when I try and load an annotation in freeview, the rh loads properly (looks normal and is on the correct hemisphere), but the lh loads onto the rh and is tye-died in appearance.

Can you help with this?

Thanks,

Laura

---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Date: Wed, Dec 18, 2013 at 2:14 PM Subject: Re: [Freesurfer] Problems dipslaying annotations in freeview

Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu

oh, if the lh annot is being loaded onto the rh surface, then that will definitely create the tye-died appearance.*Maybe Ruopeng can weigh in on the freeview issue.*

doug

On 12/18/2013 04:53 PM, Laura wrote:

Hi Douglas,

I would go to the annotation drop down menu in freeview, select
l/rh.aparc.a2009s.annot and then it would freeze.  I can't seem to
reproduce that problem today, but for every subject that I load an
annotation for now, the rh annotation loads properly,*but the lh
annotation loads onto the right hemisphere and is tye-died in
appearance.*

Thanks,

Laura


On Tue, Dec 17, 2013 at 11:57 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:


    So when you say you cannot load it, what do you mean?
    doug




    On 12/17/2013 02:55 PM, Laura Taylor wrote:

        Hi Douglas,

        I checked the status of each subject once recon-all was
        completed (by looking in the terminal window before I closed
        it).  Each of my roughly 90 subects had the message
        "/recon-all -s/ subjectID /finished without error/ at date and
        time".


        When I look at the recon-all.log file the same message is
        there at the end.  Is there somewhere else where i should look
        for an error message??

        Thank you,
        Laura


        On Tue, Dec 17, 2013 at 10:44 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>>
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<mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> wrote:


            For the subject that you were not able to load the annot,
        did you
            check the recon-all log file? Did recon-all complete
properly?
            doug


            On 12/17/2013 01:35 PM, Laura  wrote:

                Hi again, Douglas and freesurfer experts.

                Unfortunately my problem cannot be explained by having
        made
                manual edits and then not finishing recon-all.  When I
        load
                subjects that I did not manually edit, I am either
        unable to
                load an annotation file (specifically
        r/lh.aparc.a2009s.annot)
                at all, or I can load it but have problems with the
        output.
                 When I am able to load an image I get a the same
tye-died
                appearing surface for one hemisphere (and it is
        projected onto
                the opposite hemisphere that the label is for) or
I get a
                proper surface when I load the label for the other
        hemisphere
                (and it appears on the correct hemisphere).

                Can  you help at all with this?

                Thank you,

                Laura


                On Tue, Dec 10, 2013 at 11:45 AM, Laura Taylor
>>>> wrote:

                    Hi, yes thank you both.  That is exactly what the
        problem was.

                    Laura


                    On Tue, Dec 10, 2013 at 11:12 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>>
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<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>>>>> wrote:

                        Yep, looks like your annot is out of sync
with the
                surfaces

                        On 12/10/2013 01:51 PM, Chris Watson wrote:
                        > I've seen this happen after making manual
        edits and
                then not
finishing
                        > a re-run of recon-all.
                        > Chris
                        >
                        > On 12/10/2013 02:00 PM, Laura Taylor wrote:
                        >> Hi,
                        >>
                        >> I'm trying to load lh.aparc.a2009s.annot
        onto the
                lh pial
                        surface of
                        >> a subject.  When I use the freeview gui and
        select
                        >> lh.aparc.a2009s.annot under the annotations
        menu a
                strange
                        >> multicolored surface is loaded.  It
looks like
                something
                        that has
                        >> been tie-dyed and not like the examples of
        parcellation
                        that are
                        >> shown on some of the freesurfer pages.
                        >>
                        >> I have attached a screenshot of the output
        that I get.
                        >>
                        >> Any help would be appreciated.
                        >>
                        >> Thank you,
                        >>
                        >> Laura
                        >>
                        >>
                        >>
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