Dear AFNI experts,
I hope everyone is well! I have a (hopefully quick) question about the output of 3dGroupInCorr.
I ran:
cd "$deriv_dir" # change directory to where pre-processed files are
# define prefix
out_GroupInCorr=FC_task-"$task"_wholebrain_pearson
# set up FC
3dSetupGroupInCorr -mask $code_dir/$epi_mask_rest -prefix "$FC_dir"/$out_GroupInCorr -byte ./sub-*/func/*_task-"$task"_desc-fullpreproc_bold.nii.gz
cd "$FC_dir"
3dGroupInCorr -setA "$FC_dir"/$out_GroupInCorr.grpincorr.niml -verb -batch MASKAVE "$code_dir"/seeds_MMC
This creates an output file for each of my seeds (seedFC_*+trlc.) with 2 sub-bricks #0 FC_task-rest_mean and #1 FC_task-rest_Zscr.
Is it correct that what is shown in the 0th sub-brick shows the mean of arctanh(correlation)?
If so, is it correct to run the code below to create a #2 sub-brick containing the actual correlation values to use for, e.g. thresholding?
for (( r=0; r<${num_seeds}; r++)); do
echo "${seeds[$r]}"
# 0th sub brick shows mean of arctanh(correlation)
# 1st sub brick shows Z score of t-statistic for above mean
3dcopy ${seeds[$r]}+tlrc all_${seeds[$r]}+tlrc
# compute actual correlation values
3dcalc -a all_${seeds[$r]}+tlrc[0] -expr 'tanh(a)' -prefix corr_${seeds[$r]}
# append volume
3dTcat all_${seeds[$r]}+tlrc -glueto corr_${seeds[$r]}+tlrc
done
The volume corr_seedFC_*+trlc then has three sub-bricks as output (#0 FC_task-rest_mean #1 FC_task-rest_Zscr #2 FC_task-rest_mean. This is the output of 3dinfo for each sub-brick:
3dinfo -dmin -dmax corr_seedFC_*[0]
-0.155135| 1.77568|
3dinfo -dmin -dmax corr_seedFC_*[1]
-8.48432| 13|
3dinfo -dmin -dmax corr_seedFC_*[2]
-0.153903| 0.944229|
Is it hence correct that they show the mean of arctanh(correlation), the Z score of t-statistic of the mean, and the mean of correlation respectively? I just want to make sure that I did not mess up my data before thresholding the maps based on the correlation maps.
Your insight is as always highly appreciated!
Thanks in advance,
Stef
