Thank you Bruce,

I read that mris_sample_parc "samples a volumetric parcellation onto a surface". 

I understand that this is like creating from a file of the type of aseg a corresponding file of the type of aparc.annot.ctab. 

Is this not true? Do I actually  have to create the aparc.annot.ctab type file manually and give this as the above mentionned file to the command? The file is only an optional arguement though?

Thanks again, Markus


2013/12/14 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Hi Markus

you need to create that file (or update FreeSurferColorLUT.txt) to reflect whatever you have in /Documents/myROIfile.mgz

cheers
Bruce


On Sat, 14 Dec 2013, Markus Gschwind wrote:

Dear Bruce,
Thank you for your answer. I have not yet gotten it correctly.

1) Where does that file come from? Should I create it? how?

2) what is missing in the command of mris_sample_parc? Why does it now
work? 

3) what does the second error mean?
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory

Thanks in advance!
[cleardot.gif]

Markus


2013/12/13 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
      Hi Markus

      that file translates indices/annotations into colors to display
      and human reasable names.

      cheers
      Bruce
      On Fri, 13 Dec 2013, Markus Gschwind wrote:

            I can precise the question, actually there are
            three:

            1) ist the command correct?

                  mris_sample_parc -v -sdir subject001 rh
                  ~/Documents/myROIfile.mgz rh.myROIfile.annot


            2) I do not understand the meaning of this claimed
            file
            cma_parcellation_colors.txt

            Actually this does not exist. In the Wiki
            (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_sample_parc)
            it says that
            there was an optional arguement

            -file <filename>

            use <filename> as translation (default:
            'cma_parcellation_colors.txt')


            If I understand correctly, "translation" points ot a
            problem of different
            spaces, but the filename rather seems something like
            a parcellation/atlas
            color table?

            3) The result of this problem seems to be that I
            cannot annotate the surface
            using the created annotation file. It gives this
            error, which i do not
            understand.



            CTABfindAnnotation: ct was NULL
            No such file or directory
            CTABfindAnnotation: ct was NULL
            No such file or directory
            CTABfindAnnotation: ct was NULL
            No such file or directory
            CTABfindAnnotation: ct was NULL
            No such file or directory
            ... etc.

            Can anyone help me find the problem?


            Thank you in advance!

            Markus 




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