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.gschw...@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 <fis...@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 <fis...@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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