Re: [Freesurfer] problem creating annotation using mri_sample_parc?

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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