Hi Donna, Yes! I was able to successfully get past the issue of JRE halting-- I just installed the latest JRE as Tim suggested, and added some options for garbage collection so that it would optimize memory use. Thank you for all your help!
I have computed one mean midthickness for all my subjects, but specifically how do I overlay that onto an anatomical template? Would there be any advantage of using the NIFTI volume vs. using an average volume created from my subject pool? If so, how would I be able to generate that average volume? I am also a bit unclear on how to interpret and draw conclusions from the outputs of TFCE. I understand that TFCE creates many .metric files including one that indicates all the significant differences between the two groups. How can I overlay that (along with the .label file) onto a surface in Caret? (Where does the mean midthickness come into play?) Also, how do I interpret the results written in the significance.report text file? Thank you so much. Sincerely, Eshita On Thu, Jan 30, 2014 at 5:17 PM, Donna Dierker <[email protected]>wrote: > Wow, does this mean you got past the grind-to-a-halt JRE problem? > Excellent! > > Here is a script I used to compute mean midthickness surfaces for two > groups: > > > http://brainmap.wustl.edu/pub/donna/US/UCLA/ESHITA/gen_mean_fiducials.pared.sh > login pub > password download > > But the main command is this one: > > caret_command -surface-average $OUTCOORD $COORD1 $COORD2 ... $COORDn $SHAPE > > The $SHAPE is a vertex:scalar mapping identical in format to a metric, but > it stores the 3D variability for each vertex. > > You can visualize multiple mean coord files (e.g., one for each DX group) > overlaid on the same anatomical volume (e.g., avg152T1) and click on hot > spots on your metric, to see if the contours diverge there. You can also > compute the distance between the two surfaces directly on the Surface: > Measures menu (if I recall correctly). > > Sounds like you're making great progress! > > > On Jan 30, 2014, at 5:27 PM, Eshita Shah <[email protected]> wrote: > > > Hello, > > > > I have created metric files from my TFCE statistical analysis that I > wish to view on my own study-specific generated average coordinate file. > How would I go about doing so? I do have the Conte69 Visualization Atlas, > but I am not sure how to overlay the metric files generated by TFCE to > visualize significant clusters. I would eventually like to do this overlay > on my own average file, not the 164k averages. > > > > Thank you, > > Eshita > > > > -- > > Eshita Shah > > University of California, Los Angeles | 2014 > > B.S. Neuroscience > > [email protected] > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > -- Eshita Shah University of California, Los Angeles | 2014 B.S. Neuroscience [email protected]
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