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
