Hi Jennifer,
do you need a table file? I thought not, since the color table is embedded in the .annot file. If you give it an output directory it should extract a label for every different structure in the .annot file. The label file columns are:
<1> vertex index <2>-<5> surface RAS coordinates of the vertex, I believe from the orig surface (could be white, I'm not positive) <6> a slot to assocate a statistic with that vertex (e.g. fMRI p-value)
Does that answer your questions? I'm not sure...
cheers, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
I'd like to retrieve information wrt XYZ coordinates of vertices within aparc labels.
I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s
A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?)
Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label
Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc
- What is the name & location of the table file I should be specifying
to return all 94 labels? Or do I need to include additional flags in my command line? 2) How are the columns ordered within each output file generated by the mri_annotation2label command?
I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Many Thanks, Jenifer
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