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
