Hi Doug,

I ran make_average_surface.no-aparc and identity matrices on my data, and I seems to have completed the averaging without an error. However, when I try to view the result with tksurfer, I get an error because there is no average T1 for the average subject. How would you recommend I go about this? Do you have a make_average_volume.no-aparc as well, shall I make an average T1 manually, or can I skip the average T1?

Thanks!
Caspar

2013/8/19 Douglas N Greve <greve@nmr.mgh.harvard.edu>

I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run

tkregister2 --fstal --s subject

It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity

doug

On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
that's great, thank you very much.
From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that?
Thanks, Caspar

2013/8/19 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>

    I've put that script here

    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc


    On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote:
    > Hi Freesurfer experts,
    > I am trying to make an average surface from several monkey surfaces,
    > and I ran into a problem with make_average_subject.
    Specifically, I do
    > not have an aparc file nor a talairach.xfm. It seems that these
    > problems have come up on the list before
    >
    (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html).
    > I tried to download make_average_surface.no-aparc, however, the link
    > seems to be broken. Also, I couldn't find a solution to the missing
    > talairach.xfm on the list.
    > It would be great if you could provide me with a working link to
    > make_average_surface.no-aparc; any suggestions regarding making an
    > average surface without talairach.xfm would be appreciated.
    > I already made a new template and aligned all individual surfaces to
    > this template.
    >
    > Thanks!
    > Caspar
    >
    >
    >
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    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center

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

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