Hi (Doug, Kevin, ...),
I am experiencing a problem with making labels in Tksurfer (for doing a subsequent ROI analysis). I did something as follows:
1) I loaded a functional activity map by surf-sess (human cortex).
2) Then, I loaded the full flattened cortical surface.
3) After right-clicking in the Tksurfer window, I clicked (left-clicking) on the center of 4 spatially distinct activity patches (i.e. 4 yellow spots of activity, which had no overlap with each other and no overlap with other yellow or blue patches). So 4 vertices were selected (as I saw in the command-line window).
4) Then, I openned the "Custom Fill" dialog box, and selected the following options:
Fill Conditions: Up to and including paths, Up to functional values below threshold
Fill From: All marked vertices
Action: Create a new label
After clicking the "Fill" button (in the "Custom Fill" dialog box) and then clicking the "Mark Label" button (in the Tksurfer window), the 4 patches were appropriately selected as white labels. In the command-line window:
% surfer: filling (ctrl-c to cancel).. done, 123 vertices filled surfer: filling (ctrl-c to cancel)... done, 542 vertices filled surfer: filling (ctrl-c to cancel). done, 105 vertices filled surfer: filling (ctrl-c to cancel)..... done, 954 vertices filled
5) I saved the selected label. In the command-line window:
writing 2913 labeled vertices to /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects/katie/label/DFPRHKAS.label.
The problem is that the number of saved vertices is much more than the sum of vertices in the 4 patches (2913 vs. 123+542+105+954). I do not have this problem when I click on just 2 patches (rather than 4), and the number of saved vertices is the sum of vertices in the 2 patches. I also had this problem before, and I am worried that some additional vertices (voxels) are saved out of my control, which might affect the ROI analysis.
Thanks for any help,
Best, Reza
******************************** Reza Rajimehr, MD
NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129
Email: reza@nmr.mgh.harvard.edu ********************************