Hi all!

I've figured out how to use 3dTcorr1D, but I would like to learn how to use 3dNetCorr so that I can run multiple ROIs at once for resting state functional connectivity analysis.

The steps I use for 3dTcorr1D are as follows:
#create 5mm radius ROI around peak fmri task activation
3dUndump -prefix task_5mmROI -master $subj_anat+tlrc. -srad 5 -orient RAI -xyz task_peak_xyz.txt
#resample ROI mask to match volumes of data set
3dresample -master $subj_rest_run1.nii.gz -prefix task_resamp -inset task_5mmROI+tlrc.
#use resampled mask to extract time series of ROI and redirect output to 1D file
3dmaskave -mask task_resamp+tlrc. $subj.rest_run1.nii.gz > maskave_taskROI.1D
#pearson correlation for input data set and 1d file of time series for ROI
3dTcorr1D -mask $subj.REF.mask.FBrain.MNI.nii.gz -prefix Tcorr_rest_run1_taskROI -ok_1D_text $subj.rest_run1.nii.gz maskave_taskROI.1D

This is the example I tried to take from 3dNetCorr -help :
3dNetCorr \
-inset $subj.rest_run1.nii.gz \
-in_rois ?????? NEED HELP????? \
-fish_z \
-ts_wb_corr \
-mask $subj.REF.mask.FBrain.MNI.nii.gz \
-prefix FMRI/REST_corr

how do I create the ROI time series file differently for 3dNetCorr? Do I still need to do 3dmaskave as a step? If so, how do I transform that output to .BRIK/.HEAD files?


Thank you!!