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
