I emailed Eshita off-list yesterday, because the message contained pre-publication data.
On Feb 7, 2014, at 4:07 PM, Eshita Shah <[email protected]> wrote: > 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] > > > _______________________________________________ > 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
