Hi,
We need to display surface data (.w file). However, our algorithm failed to assign values for some vertices (and were therefore given the value of exactly zero), and to clearly differentiate those from vertices where we successfully computed values, we would like the vertices where we could not compute a value to be blank (=only the underlying anatomical surface shows).
Normally I would just threshold the values to get rid of the "blank" vertices. However, we want to use tksurfer "offset 0.5" to shift the distribution such that all values smaller than 0.5 are shown as blue and all values larger than 0.5 in red/yellow. The offset also has the effect that the vertices where we were unable to compute a value will now have a value of exactly -0.5.
Then, the question becomes how to make tksurfer paint only the vertices where we have a successfully computed value. After the shift, thresholding will no longer work because it only operates on values around zero.
We have tried editing the .w file by both (i) removing the values from the vertices that we do not want painted, and (ii) removing the vertices (the entire line, vertex index plus value) from the file, but the tksurfer brain surface window still shows an overlay with a value of 0 in these vertices.
Thanks!
Tommi
--- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
Hi Tommi, nothing comes to mind in terms of buttons to press on tksurfer. Can you just add .5 to the non-zero voxels in the w-file? Then you don't have to use the offset. doug
On 04/09/2013 03:23 PM, raij@nmr.mgh.harvard.edu wrote:
Hi,
We need to display surface data (.w file). However, our algorithm failed to assign values for some vertices (and were therefore given the value of exactly zero), and to clearly differentiate those from vertices where we successfully computed values, we would like the vertices where we could not compute a value to be blank (=only the underlying anatomical surface shows).
Normally I would just threshold the values to get rid of the "blank" vertices. However, we want to use tksurfer "offset 0.5" to shift the distribution such that all values smaller than 0.5 are shown as blue and all values larger than 0.5 in red/yellow. The offset also has the effect that the vertices where we were unable to compute a value will now have a value of exactly -0.5.
Then, the question becomes how to make tksurfer paint only the vertices where we have a successfully computed value. After the shift, thresholding will no longer work because it only operates on values around zero.
We have tried editing the .w file by both (i) removing the values from the vertices that we do not want painted, and (ii) removing the vertices (the entire line, vertex index plus value) from the file, but the tksurfer brain surface window still shows an overlay with a value of 0 in these vertices.
Thanks!
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-
Douglas N Greve -
raij＠nmr.mgh.harvard.edu