No, I think the problem is that nothing survived TFCE thresholding. If it had, you would see an entry (or more) under the column heads (Column, Thresh, Num-Nodes, etc.). There is no entry, which means nothing survived.
Column Thresh Num-Nodes Area Area-Corrected COG-X COG-Y COG-Z P-Value TFCE P You can try loading your f-map (ANOVA_29-01-14.OCD_CTRL.Depth.LH.fmap.significant.tfce.1.0E.2.0H.73730.metric) and switch to the TFCE column, and apply thresholds corresponding to the list of values right under the column heads, so you can see how close/far you were. I am under the weather right now, so I will have another look at this tomorrow, but I honestly think you are interpreting it correctly. If you are like me, you probably are disappointed with these results. (There are exceptions, of course.) On Feb 3, 2014, at 4:37 PM, Eshita Shah <[email protected]> wrote: > 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 <[email protected]> > 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 <[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 > > > _______________________________________________ > 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
