Dice metric/coefficient

AFNI Message Board
1

Hello,

I have performed a seed-based analysis in young and aged monkeys and have the resulting t-maps for each individual monkey as well as group t-maps t-tested against 0. I wanted to look at the variance between individual aged monkeys and the group t-map for young monkeys to plot the variance against behavioral score to see whether there is a correlation between greater variance (from young) and worse performance. I thought using a dice coefficient would work but based on the message board, I am thinking this is mostly for overlap of binary masks and not necessarily t-stats. If this is not the correct program, perhaps you can recommend something?

When I run @DiceMetric (@DiceMetric -base young_tmap+tlrc -dsets old_1_tmap+tlrc old_2_tmap+tlrc… ), i get a .1D file for each of the 18 monkeys but it doesn’t contain any information:

#cl #dice(PATH/SUB/SUB_clust_1_blur3.nii.gz VS PATH/young_clust_1_all_map)
#Labels:

I am not sure what the aib.1D file output is but that looks like this:

#	Mean_1  	NZcount_1	Mean_2  	NZcount_2	Mean_3  	NZcount_3	Mean_4  	NZcount_4	Mean_5  	NZcount_5	Mean_6  	NZcount_6	Mean_7  	NZcount_7	Mean_8  	NZcount_8	Mean_9  	NZcount_9	Mean_10  	NZcount_10	Mean_11  	NZcount_11	Mean_12  	NZcount_12

#AFN_uijqgwRzaW4l5kXc9hZmZw.aib+tlrc 0[SetA_mean]
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#AFN_uijqgwRzaW4l5kXc9hZmZw.aib+tlrc 1[SetA_Zscr]
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#File Sub-brick
# Mean_1 NZcount_1 Mean_2 NZcount_2 Mean_3 NZcount_3 Mean_4 NZcount_4 Mean_5 NZcount_5 Mean_6 NZcount_6 Mean_7 NZcount_7 Mean_8 NZcount_8 Mean_9 NZcount_9 Mean_10 NZcount_10 Mean_11 NZcount_11 Mean_12 NZcount_12
#/NAS/1_Rapp_Unit/Ciana/Sharyn_fc_cb_results/young_clust_1_all_map+tlrc 0[SetA_mean]
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#/NAS/1_Rapp_Unit/Ciana/Sharyn_fc_cb_results/young_clust_1_all_map+tlrc 1[SetA_Zscr]
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#File Sub-brick
# Mean_1 NZcount_1 Mean_2 NZcount_2 Mean_3 NZcount_3 Mean_4 NZcount_4 Mean_5 NZcount_5 Mean_6 NZcount_6 Mean_7 NZcount_7 Mean_8 NZcount_8 Mean_9 NZcount_9 Mean_10 NZcount_10 Mean_11 NZcount_11 Mean_12 NZcount_12
#/NAS/1_Rapp_Unit/Sharyn/NHP_aging/thelma/NEW_MASK_thelma_clust_1_blur3.nii.gz 0[clust_1_R]
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

When I include the -save_diff option, I get an output dataset but no actual number to represent the coefficient.

I appreciate your help in advance.
Thanks!
Sharyn

2

@DiceMetric is a script that expects masks as input, and there can be multiple masks per dataset (1,2,3,…). Consider masking the data separately to a create a binary dataset that is your mask or using 3dABoverlap to compute overlap of two datasets. There’s no Dice coefficient there though.


3dABoverlap -no_automask [i]dset1 dset2[/i]

Use the -no_automask dataset if the dataset has already been thresholded, or take it out if it hasn’t.

3

For simple cases of binary masks, consider 3ddot -dodice, perhaps using what is done in a proc script for example.

  • rick