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