Julia,
I looked at your report and your t-map, which is consistent with the
caret_command -metric-information output you included below.
Just making sure you understand this part of the report:
TMap
----
Column Thresh Num-Nodes Area Area-Corrected COG-X COG-Y
COG-Z P-
Value
1 2.500 3064 2223.228027 2245.943848 -30.317 -73.796
-12.228 0.0
12000
1 2.500 3372 1865.999878 1863.883423 -21.516 -62.842
46.382 0.0
17000
1 2.500 1557 681.308838 674.981384 -32.967 -5.873
48.701 0.0
59000
These are the clusters in your real t-map that were significant at the 0.1
alpha you specified, using the 2.5 threshold. (Note that all the significant
clusters were at the positive end.)
I believe the reason you saw different max/min in the Caret GUI was that you
had the permuted t-map loaded, instead of the real one. In your message below,
you said, "Adjustment:Column: permuted T-Values,Threshold type". There is
nothing about permuted in the file you uploaded. If you were viewing the
permuted/shuffled t-map, this would also explain why little would survive a low
threshold.
But we don't necessarily (or even usually) use the same values we used for
cluster thresholds as the threshold for displaying t-maps, e.g., for
publication purposes. I think we like to see some color differentiation beyond
the cluster threshold max. If they are the same, the color will saturate at
the max. Sometimes we'll use a p-value derived from the degrees of freedom and
get a corresponding t-value from that, and use that for thresholding. Other
times we might just use, say, +/-4.0 or higher, depending on how big the values
get in the data. Usually we'll use a symmetric scale (i.e., -x to +x -- rather
than different min/max).
Donna
On 08/11/2010 09:12 AM, Julia Bender wrote:
> Hi Donna,
>
> I've just uploaded the two files.
>
> Thanks for your help!
>
> Julia
>
>> Julia,
>>
>> It will be easier for me to get my head around your question if I can
>> get two files:
>>
>> * T-Map_LH_cCue_Endo.metric_TMap.metric (whatever the final output
>> metric was, but NOT the permuted/shuffled tmap file).
>>
>> * The report named something like *Signicance*.txt
>>
>> Could you upload those here:
>>
>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>
>> My brain would be ever so grateful.
>>
>> Donna
>>
>> On 08/11/2010 07:07 AM, Julia Bender wrote:
>>
>>> Hey everyone,
>>>
>>> I'm a bit confused about how to threshold my T-Maps in caret5. I created
>>> the maps with the following command:
>>>
>>> /usr/local/caret/bin_linux/caret_command
>>> -metric-statistics-one-sample-t-test $EACHMETRIC $FIDUCIAL_COORD
>>> $OPEN_TOPO $SURFACE_SHAPE 3 T-Map_$EACHMETRIC -300000.0 2.5 0.10 10 1
>>> 1000
>>> 0 4
>>>
>>> So I put the negative threshold to -300000 and the positive threshold to
>>> 2.5. When I look at the resulting Tmap.metric files it gives me
>>> something
>>> like this:
>>>
>>> Filename: T-Map_LH_cCue_Endo.metric_TMap.metric
>>> Number of Nodes: 73730
>>> Number of Columns: 1
>>> Column Minimum Maximum Mean Sample Dev %
>>> Positive % Negative Column Name
>>> 1 -9.785 6.076 -0.950 2.639
>>> 36.234 63.766 T-Values
>>>
>>> As far as I understand, this means the maximum negative T value in this
>>> metric is -9.785 and the maximum positive T value is 6.076. When I open
>>> the file in caret though (Color mapping: Auto Scale, Display mode: Both,
>>> Display Color Bar, Threshold Adjustment:Column: permuted
>>> T-Values,Threshold type: Column) the bar tells me that my maximum
>>> negative
>>> value is -3.7 and my maximum positive value is 2.6. This also holds when
>>> I
>>> adjust the thresholds in the fields below to -2 and 2, when almost all
>>> activation disappears.
>>>
>>> Which is the correct information?
>>>
>>> Thanks a lot for your help!
>>>
>>> Julia
>>>
>>>
>>>
>>>
>>> Dipl. Psych. Julia Bender
>>> Humboldt Universität zu Berlin
>>> Mathematisch - Naturwissenschaftliche Fakultät II
>>> Institut für Psychologie, Abt. Klinische Psychologie
>>> Unter den Linden 6
>>> D-10099 Berlin
>>>
>>> _______________________________________________
>>> 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
>>
>>
>
>
> Dipl. Psych. Julia Bender
> Humboldt Universität zu Berlin
> Mathematisch - Naturwissenschaftliche Fakultät II
> Institut für Psychologie, Abt. Klinische Psychologie
> Unter den Linden 6
> D-10099 Berlin
>
> _______________________________________________
> caret-users mailing list
> [email protected]
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
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