On Jan 31, 2014, at 2:17 PM, Eshita Shah wrote: > 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?
One advantage of using the template used for stereotaxic/volumetric registration, if any was done, is that it is standard. Reviewers and readers are more familiar with it, and don't have to understand how it was generated. This is just for display/orientation -- not for analysis. Another is that you don't have the extra step of computing a mean volume. > f so, how would I be able to generate that average volume? I usually use AFNI's 3dMean when I need to do this, but FSL, SPM, and other packages have similar features. Maybe wb_command supports it now. You can probably do it in multiple steps with caret_command, but it's a pain. > 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? I usually generate a border about the cluster in the label.gii file and overlay it on the unthresholded t-map, so that users can see subthreshold diffs. I display the t-map on the inflated atlas surface (Conte69, if I recall correctly here). If there are diffs in the insula/operculum, i use the very inflated surface, which shows them more clearly. > (Where does the mean midthickness come into play?) Sometimes it is evident just by comparing the mean midthickness surfaces that there is a difference. Other times, you need to look at a slice view of the template with group contours overlaid at a slice that best shows the diffs. Could be coronal, axial, or sagittal. > Also, how do I interpret the results written in the significance.report text > file? If you upload your report, I can tell you the lines to focus on: http://brainvis.wustl.edu/cgi-bin/upload.cgi They should be near the top, just below a header that lists the column, number of nodes, corrected and uncorrected areas, x, y, z, etc. I'm psyched you got this far! I was feeling frustrated after you ran into the JRE problem. I'm glad you got past it. > 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] > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users
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