Re: [Freesurfer] problem creating annotation using mri_sample_parc?

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! 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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