[caret-users] Visualization in Caret

Eshita Shah eshshah at ucla.edu
Mon Feb 3 16:37:06 CST 2014


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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>> > caret-users at brainvis.wustl.edu
>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
>>
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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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