Re: [Freesurfer] problem creating annotation using mri_sample_parc?

Hi Markus

for example, this is what is in the one we use:

mris_info $FREESURFER_HOME/average/lh.destrieux.simple.2009-07-29.gcs reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized GCSA file /cluster/p41/fischl/dev/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs opened 0 Unknown 0 0 0 0 1 G_and_S_frontomargin 23 220 60 0 2 G_and_S_occipital_inf 23 60 180 0 3 G_and_S_paracentral 63 100 60 0 4 G_and_S_subcentral 63 20 220 0 5 G_and_S_transv_frontopol 13 0 250 0 6 G_and_S_cingul-Ant 26 60 0 0 7 G_and_S_cingul-Mid-Ant 26 60 75 0 8 G_and_S_cingul-Mid-Post 26 60 150 0 . . .

it translates between an index (e.g. 1), a human readable name (G_and_S_frontomargin) and an rgb value for displaying on the surface (23 220 60). You would have the indices in your volume, then this color table would translate it into values to display on the surface.

Make sense?

Bruce

On Mon, 16 Dec 2013, Markus Gschwind wrote:

Dear Bruce or someone else, would you mind answering a little more in detail, please? I am stuck. There is hardly any thread about the command mris_sample_parc, but I need this function.

1. This file called "cma_parcellation_colors.txt", is an option for mris_sample_parc. Where does that file come from? How am I

supposed to create it?

2. What is missing if the loading of the created annotation file onto a surface (in freeview) gives the following error,

repeating for infinity 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

What does this error mean, at all?

Thank you and please excuse my insisting! Markus

2013/12/14 Markus Gschwind markus.gschwind@gmail.com 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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