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: >> >> 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: [EMAIL PROTECTED] >> ******************************** >> _______________________________________________ >> 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: [EMAIL PROTECTED] ******************************** _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
