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Hi Mark sorry for the late reply. I am doing resting state data analysis. I am using ABIDE data that is publicly available (the download is 2 files. 1 anatomical (Mprage) and 1 functional (rest)). I thought I overcome this problem with the following steps: 1) BET extract Mprage 2) Run Feat 3) Convert filtered_func file into MNI 152 standard space using Flirt option 4) Generate ROI which is made in standard 152 space 5) Extract time course from this ROI using my newly generated standard_space_filtered_func file 6) Convert the Mprage_brain into standard space 7) FAST segmentation using standard space Mprage brain and standard space tilt fund file. 8) Extract time course of the White matter and CSF into .txt files 9) use the CSF, WM time course .txt files and input them as EVS to regress out of my ROI time course. I have selected orthogonalise, temporal derivative and temporal filter for the ROI EV but not for the two nuisance regressors. 10) Use the newly generated .feat file in a group level analysis. My main concerns are: 1) Will transforming my data into standard space like this change my data? 2) Is it correct to select the temporal derivative and temporal filter options in step 9? Could you please tell me if this pipeline seems reasonable or not? Thanks