Donna, Thank you so much for your thorough response. What I'm worried about as of now is the significance.report.txt file. I have uploaded it using the link you provided, please let me know if there is anything unusual. When I ran ANOVA without TFCE, I had rows of information right below the header, as you mentioned. But for the TFCE report, I don't see anything similar. Maybe I am interpreting it incorrectly?
Thank you, Eshita On Fri, Jan 31, 2014 at 1:15 PM, Donna Dierker <donna.dier...@sbcglobal.net>wrote: > 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 < > donna.dier...@sbcglobal.net> 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 <eshs...@ucla.edu> 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 >> > eshs...@ucla.edu >> > >> > >> > _______________________________________________ >> > caret-users mailing list >> > caret-users@brainvis.wustl.edu >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > > > -- > Eshita Shah > University of California, Los Angeles | 2014 > B.S. Neuroscience > eshs...@ucla.edu > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > -- Eshita Shah University of California, Los Angeles | 2014 B.S. Neuroscience eshs...@ucla.edu
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