Thanks again for the info. However, I'm still not sure how to get an
ascii file for each aparc label listing the vertex index, and the RAS
coordinates (surface RAS is fine since I can use the fscoordinates.pdf
and the wikipage on Coordinate systems to get back to vol coordinates
and eventually scanner coordinates.)
Any suggestions how to access this information? From the help pages, I
thought mri_annotation2label would do the trick...
Jenifer
-----Original Message-----
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu]
Sent: Monday, October 01, 2007 1:05 PM
To: Bruce Fischl
Cc: Juranek, Jenifer ; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc
labels
I don't have code to do it, but you can look at this doc:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=Attac
hFile&do=get&target=fscoordinates.pdf
which explains how to get back to scanner coords
doug
Bruce Fischl wrote:
yes, I think Doug has documented how to do this on our wiki. Doug: can
you point jenifer at the right place?
thanks,
Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
Hi Bruce,
Many thanks for the information.
Yes, I'd like a table file for each aparc label in each hemisphere.
Whether the annotation file is the ?h.aparc.a2005s.annot variety or
the
?h.aparc.annot variety is not crucial at this point.
My goal is to map the XYZ vertex coordinates for each aparc label
back
to the scanner XYZ coordinates. Is this possible?
Jenifer
-----Original Message-----
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]
Sent: Monday, October 01, 2007 10:25 AM
To: Juranek, Jenifer
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc
labels
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
1) 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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