Hi Don
try mri_label2label. Also, the if you are transforming label volumes you
need to use nearest neighbor interpolation, so include the -rt nearest
switch.
cheers
Bruce
On Fri, 1 Aug 2014, Krieger, Donald N. wrote:
Hi All,
I am still in need of finding the tool sequence to generate an ASCII file
containing (1) voxel RAS coordinates (2) for a specific label (3) using the
original MRI coordinates rather than freesurfer coordinates.
mri_convert -rl rawavg.mgz <input vol> <output vol>
does generate a new output volume containing the “labelled” voxels contained
in <input vol> . I can tell because this volume shows up more or less
correctly in freeview although the color mapping appears to have changed or
perhaps freeview is doing some kind of “fill” operation differently
depending on the loaded volume. I assume these are in the coordinates for
rawavg.mgz but cannot tell for sure.
I need to generate a list of these voxel coordinates from <output vol> to
check and for my work.
(1) Do I need to generate a new annotation file from <output vol> and
then use mri_annotation2label to get there? I have not been able to find
the tool sequence which generates the .annot files.
(2) An alternative appears to be mri_label2label with –xfm xfmfile and
possibly including --xfm-invert . I did get this command to complete
successfully using mri/transforms/talaraich.xfm but I presume this is not
the correct transform.
Thanks and best regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
From: Krieger, Donald N.
Sent: Thursday, July 31, 2014 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: YANQ follow-up
Thanks again for the pointer, Bruce.
You wrote:
… mri_convert -rl rawavg.mgz <input vol> <output vol>
which does produce an output volume from which I now need to extract RAS
voxel coordinates.
A pointer to a keyboard command would be most welcome.
Of interest is the difference between the color mappings for the input and
output volumes in freeview.
When using the lookup table in freeview they are quite different whereas in
grayscale they are almost identical.
I wonder if this is contributing to my difficulty in finding a tool to
extract the voxel coordinates.
Thanks again.
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
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