Hi Sahil,

When you check the Setup>Options>Create Confoud corrected time-series option, the toolbox will create nifti files containing the BOLD times series for each voxel after removing of confounding effects, filtering, and concatenating across all of the repetitions for each condition. Those should be located in the folder

conn_*/results/preprocessing/

and named as niftiDATA_Subject###_Condition###.nii files (one file per subject/condition).

If what you want instead is to have the same timeseries but for each ROI (not for each voxel), then you can simply find these in the same folder but named as

ROI_Subject###_Condition###.mat files (one per subject/condition)

(and you do not need to have the Setup>Options>... option checked for these to be created, these are always created as long as you are performing ROI-to-ROI analyses). Within these files you will find a variable named 'data' containing the timeseries for each ROI, and a variable named 'names' containing the associated ROI names. 

Hope this helps
Alfonso
Originally posted by Sahil Bajaj: