Hi Donna, I've looked more into the "caret_command -metric-statistics-one-sample-t-test" output files. I'm having trouble understanding what all the information means. Maybe you can correct me:
1. xx.metric_TMap.metric: Map of T-Values for the wholebrain (?) for the contrast defined in the xx.metric input files. Those are T-Values exceeding the T-Value thresholds and alpha level I specified in "caret_command-metric-statistics-one-sample-t-test" (eg -300000 2.5 0.1 in my case). They are not corrected for multiple comparisons(?). This is the one I should load onto my surface. When I load that TMap, why can I still see T-Values below my defined threshold? 2.xx.metric_ShuffledTMap.metric: Distribution of T-Values derived from permuting + and - on each element in xx in N iterations (in my case 1000) 3.xx.metric_TMap_Significant_Clusters.txt: This is what the help page says: "1. Find the biggest cluster in each column of the permutation T-Map metric/shape file and sort them by cluster size." I see two lists of clusters in the output file. I assume the one that is the result of this sorting is the lower one. It has about 700 rows depending on xx, why does it not have 1000 rows, one for each permutation? Are the clusters sorted by Num-Nodes, Area or Area corrected? In my files they seem kind of sorted by both... How is a cluster defined? "2. Find the largest (alpha)(iterations) clusters in the Permutation T-Map and use its cluster size as the Significant Cluster Cutoff." I assume this is the list of T-Values right below the above list of clusters, why does it contain clusters with a P-Value that is above my defined alpha? "3. Find clusters in the Real T-Map file." This must be the upper list of clusters (containing much less rows than the lower one) "4. Report all clusters in Real T-Map file that are larger than Significant Cluster Cutoff." This is the list of T-Values below this list, containing only clusters that are bigger than the cluster with the highest P-Value found in 2. that pass the alpha and T-Value thresholds I specified in "caret_command-metric-statistics-one-sample-t-test". 4. T-Map_LH_cCue_EndoL_vs_Cue_ExoL.metric_TMapClusters.metric Is this the map of clusters defined above? I'm sorry, I know these are a many questions. Thanks a lot for your help! Julia > 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 > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users Dipl. Psych. Julia Bender Humboldt Universit�t zu Berlin Mathematisch - Naturwissenschaftliche Fakult�t II Institut f�r 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
