[caret-users] Visualization in Caret

Eshita Shah eshshah at ucla.edu
Fri Feb 7 16:07:33 CST 2014


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 <donna at brainvis.wustl.edu>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 <eshshah at ucla.edu> 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 <
> donna.dierker at sbcglobal.net> wrote:
> > On Feb 5, 2014, at 4:19 PM, Eshita Shah <eshshah at ucla.edu> 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 <
> donna.dierker at sbcglobal.net> 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 <eshshah at ucla.edu> 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 <
> donna at brainvis.wustl.edu> 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 <eshshah at ucla.edu> 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 <
> donna.dierker at sbcglobal.net> 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 <eshshah at ucla.edu> 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 <
> donna.dierker at sbcglobal.net> 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 <
> donna.dierker at sbcglobal.net> 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 <eshshah at ucla.edu>
> 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
> > > > > >> > eshshah at ucla.edu
> > > > > >> >
> > > > > >> >
> > > > > >> > _______________________________________________
> > > > > >> > caret-users mailing list
> > > > > >> > caret-users at brainvis.wustl.edu
> > > > > >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > > > > >>
> > > > > >>
> > > > > >> _______________________________________________
> > > > > >> caret-users mailing list
> > > > > >> caret-users at brainvis.wustl.edu
> > > > > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >> --
> > > > > >> Eshita Shah
> > > > > >> University of California, Los Angeles | 2014
> > > > > >> B.S. Neuroscience
> > > > > >> eshshah at ucla.edu
> > > > > >>
> > > > > >>
> > > > > >> _______________________________________________
> > > > > >> caret-users mailing list
> > > > > >> caret-users at brainvis.wustl.edu
> > > > > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > caret-users mailing list
> > > > > > caret-users at brainvis.wustl.edu
> > > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Eshita Shah
> > > > > > University of California, Los Angeles | 2014
> > > > > > B.S. Neuroscience
> > > > > > eshshah at ucla.edu
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > caret-users mailing list
> > > > > > caret-users at brainvis.wustl.edu
> > > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > caret-users mailing list
> > > > > caret-users at brainvis.wustl.edu
> > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Eshita Shah
> > > > > University of California, Los Angeles | 2014
> > > > > B.S. Neuroscience
> > > > > eshshah at ucla.edu
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > caret-users mailing list
> > > > > caret-users at brainvis.wustl.edu
> > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > > >
> > > >
> > > > _______________________________________________
> > > > caret-users mailing list
> > > > caret-users at brainvis.wustl.edu
> > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > > >
> > > >
> > > > _______________________________________________
> > > > caret-users mailing list
> > > > caret-users at brainvis.wustl.edu
> > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > >
> > >
> > > _______________________________________________
> > > caret-users mailing list
> > > caret-users at brainvis.wustl.edu
> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > >
> > > _______________________________________________
> > > caret-users mailing list
> > > caret-users at brainvis.wustl.edu
> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >
> >
> > _______________________________________________
> > caret-users mailing list
> > caret-users at brainvis.wustl.edu
> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >
> > _______________________________________________
> > caret-users mailing list
> > caret-users at brainvis.wustl.edu
> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>



-- 
Eshita Shah
University of California, Los Angeles | 2014
B.S. Neuroscience
eshshah at ucla.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brainvis.wustl.edu/pipermail/caret-users/attachments/20140207/50b6ba4c/attachment-0001.html>


More information about the caret-users mailing list