Hi Kevin,
on machine monkeylove
source /usr/local/freesurfer/nmr-std-env
setenv SUBJECTS_DIR /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects
cd /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/Human_Eccen/Katie/MYSTUDY
surf-sess -sf sf.txt -df df.txt -analysis Analysis_Human_Eccen -contrast 123456 -map sig -hemi rh
I changed the min threshold to 4 (linear) in the Tksurfer window (view - config overlay ...).
Reza
Thanks for this report. Can you point me at the data you were using, whether you were using the std or dev environment, and what command you used to start tksurfer?
On Tue, Dec 12, 2006 at 11:28:45PM -0500, Reza Rajimehr wrote:
Hi (Doug, Kevin, ...),
I am experiencing a problem with making labels in Tksurfer (for doing a subsequent ROI analysis). I did something as follows:
I loaded a functional activity map by surf-sess (human cortex).
Then, I loaded the full flattened cortical surface.
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).
- 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
- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Kevin Teich
******************************** 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 ********************************