Re: [Freesurfer] problem creating annotation using mri_sample_parc?

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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