[caret-users] Visualization in Caret

Eshita Shah eshshah at ucla.edu
Tue Feb 4 20:09:00 CST 2014


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
> > >> >
> > >> >
> > >> > _______________________________________________
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> > >>
> > >>
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> > >>
> > >>
> > >>
> > >> --
> > >> Eshita Shah
> > >> University of California, Los Angeles | 2014
> > >> B.S. Neuroscience
> > >> eshshah at ucla.edu
> > >>
> > >>
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> > >
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> > >
> > >
> > >
> > > --
> > > Eshita Shah
> > > University of California, Los Angeles | 2014
> > > B.S. Neuroscience
> > > eshshah at ucla.edu
> > >
> > >
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> >
> >
> > --
> > Eshita Shah
> > University of California, Los Angeles | 2014
> > B.S. Neuroscience
> > eshshah at ucla.edu
> >
> >
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> > caret-users at brainvis.wustl.edu
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