Hi Donna, I've uploaded the metric file. I overlaid it using the inflated and very inflated coord files in Conte69 atlas (left hemisphere).
Thank you, Eshita On Fri, Feb 7, 2014 at 1:13 PM, Donna Dierker <[email protected]>wrote: > Maybe I am the one who is mistaken, but I thought this is how these > columns behaved. I would be more than happy to look at your > *significan*metric if you want to upload it: > > > http://brainvis.wustl.edu/cgi-bin/upload.cgi > > > Wow, I am jealous of your sample sizes! > > If you have only two groups, it is nice to see the polarity of the > difference, and now that you have composites (and have slogged through the > work of making your JRE work efficiently), it's just a matter of script > tweaking to get the t-test going. > > > On Feb 7, 2014, at 2:39 PM, Eshita Shah <[email protected]> wrote: > > > Donna, > > > > I may be doing something wrong, but when I change between the P and Q > columns in the "threshold adjustment" section and change the user threshold > to 0.95, 0.75, etc. as you suggested, everything remains the same. The > cluster sizes are not changing, they are the same as when I put the user > threshold to be 0.05. Is there anything else in my settings that may be > contributing to this error? > > > > I have 35 controls and 60 treatment subjects. I am looking into running > the two-sample t-test instead of anova. > > > > Thanks for your help! > > Eshita > > > > > > On Wed, Feb 5, 2014 at 3:54 PM, Donna Dierker < > [email protected]> wrote: > > On Feb 5, 2014, at 4:19 PM, Eshita Shah <[email protected]> wrote: > > > > > Hi Donna, > > > > > > I have tried changing the user threshold in the Metric Settings menu, > but nothing seems to change beyond +/- 0.05. There are a few blotches of > orange and yellow when it is at 0, and many sub-threshold regions (green) > show up when I put it up to 0.05, but nothing else changes as I move beyond > 0.05 to higher values (the orange slowly disappears, and it's all green). > > > > At least in Caret5 (less sure about workbench), thresholding won't work > properly on the p-value, because thresholding assumes more extreme values > -- further from zero -- are the more exceptional ones, whereas the opposite > is true with p-values, where the closer to 0, the more rare. Since q is > 1-p it should behave better in caret5 thresholding. If you threshold at > q=.95, you should see less than if you threshold at q=.90. Like > percentiles. > > > > > Is the value I'm changing the p or the q value? Or does that depend on > what column I have loaded in the "Threshold Adjustment" section? > > > > I'd display and threshold on both, for now, while you are trying to > understand what the data shows. > > > > > If I am changing the q value, then does it mean that the regions that > are showing up have a p-value greater than 0.95 (since nothing changes > after 0.05) and thus they're not showing up as significant in my report? > > > > If you threshold at q=.95, you should see vertices colored that have p > values of .05 or less, but you know none exist, because nothing survived in > your report. Start at q=0.5. See some vertices. Probably lots of them. > Then try q=0.75. You should see the clusters shrink now. Now 0.90. > Anything? > > > > > Let me know if I am interpreting this the wrong way. > > > > > > Also, the coloring somewhat changes depending on the color palette I > use. I believe the default is PSYCH, but when I change it to PSYCH-NO-NONE, > I see orange blots in more regions than before (and of course what was grey > earlier turns dark blue). Why is that? The "new" orange blots appear in the > same positions as the sub-threshold green color does when I change the user > threshold to 0.05. > > > > It is how the palette is defined. There is a region of the color scale > that blots out coloring near zero, while the NO-NONE removes that gap. > While my memory fails me as to why,, I remember thinking there was > something not quite intuitive about the one with the gap. Palettes are a > matter of taste to some degree. Some are better with pos/neg values, while > others are better with positive only, which is what you will have with your > f-stats. For figures, I don't use p/q-values typically, but rather t- or > f-maps. > > > > But for right now, you're doing a post-mortem on your analysis to see > how close you were to having differences, so the q-maps will be useful for > this purpose. > > > > > Lastly, how do I know which group is baseline and treatment? Does TFCE > automatically output the control group as the baseline, so the yellow would > indicate that the sulci are deeper in the treatment group vs. control? Or > the other way around? > > > > You used an ANOVA, which should produce a f-map -- all positive. There > should be no +/- valence to it, unless I'm misunderstanding what you did. > > > > Out of curiosity, how many subjects were in each group? > > > > If you have only two groups and want to see where one group is deeper > than the other, you can run a t-test instead of an anova. > > > > > Thanks for your help, > > > Eshita > > > > > > > > > > > > On Wed, Feb 5, 2014 at 5:58 AM, Donna Dierker < > [email protected]> wrote: > > > Use the D/C: Metric Settings menu to adjust the threshold to .90, .85, > etc. until you start seeing something. If you see nothing, set it to zero > and start cranking up in larger increments. Q=1-p. > > > > > > > > > On Feb 4, 2014, at 8:09 PM, Eshita Shah <[email protected]> wrote: > > > > > > > Hi Donna, > > > > > > > > What file specifically outputs the q-values and how far they are > from significance? I think I am able to load the Q statistic column from > the f-map onto the Conte69 atlas, but where should I be looking if I want > to know what to change the threshold to? > > > > > > > > Thank you, > > > > Eshita > > > > > > > > > > > > On Tue, Feb 4, 2014 at 8:32 AM, Donna Dierker < > [email protected]> wrote: > > > > Yes, pretty much: I usually have a study directory into which I > copy the Conte69 files. Then I rename the Conte69 spec to something more > study-specific. I usually use the Conte69 inflated and very inflated for > t-map visualization, along with mean group mid thickness (both > medial/lateral surface views, but also overlaid as contours on volume > slices). > > > > > > > > I don't usually use the TFCE column for visualization, and if I > recall correctly, there might be p-value and q-value (1-p, which works > better with the Caret thresholding) columns. This can tell you how close > to significance you got. > > > > > > > > And yes: You use the D/C Overlay/Underlay surface menu to control > what is displayed, which column, etc. > > > > > > > > > > > > On Feb 3, 2014, at 6:10 PM, Eshita Shah <[email protected]> wrote: > > > > > > > > > Yes, that's what I was afraid of. I was expecting significant > differences between the two groups. But thanks for clarifying. > > > > > > > > > > I am still a bit confused on how exactly to load the metric files > on the Conte69 atlas. Do I open up the Conte69 spec and "add data files" in > the menu to open up TFCE files? And then do I overlay it using D/C --> > Overlay/Underlay Surfaces --> Primary Overlay, etc.? > > > > > > > > > > Again, thank you for all your help. > > > > > > > > > > Eshita > > > > > > > > > > > > > > > On Mon, Feb 3, 2014 at 3:49 PM, Donna Dierker < > [email protected]> wrote: > > > > > 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 > > > > > > > > > > > > > > > > > > > > -- > > > > > 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 > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > > > > _______________________________________________ > > > 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 > > > > _______________________________________________ > > 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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