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
