Hi Xenios,

Thank you for your quick response!
I am so sorry I don't understand which transformation file you mean... 
Today, i tried the preprocessing step by step using the following commands, it really works well!

# 1. Motion, CSF, white, gray matter regression
bis_csfwmmotioncorr --inp ${InPath}/${subject}/rfMRI_REST.nii.gz --inp2 ${TemplatePath}/GrayWhiteCSF_mask_91_109_91.nii.gz --docsfwm 1 --usemask 1 --out ${OutPath}/${subject}/rfMRI_REST_resid.nii.gz

# 2. remove temporal Drift
bis_removetemporaldrift --inp ${OutPath}/${subject}/rfMRI_REST_resid.nii.gz --inp2 ${TemplatePath}/N12Trio_avg152T1_brain_MNI_bi.nii.gz --out ${OutPath}/${subject}/rfMRI_REST_resid_drift.nii.gz --order 1 --usemask 1

# 3. temporally smooth(zero mean, unit variance Gaussian filter)
bis_temporalsmoothimage --inp ${OutPath}/${subject}/rfMRI_REST_resid_drift.nii.gz --inp2 ${TemplatePath}/N12Trio_avg152T1_brain_MNI_bi.nii.gz --out ${OutPath}/${subject}/rfMRI_REST_resid_drift_Lpss.nii.gz --blursigma 1 --usemask 1

However, I am still confused:
1) In the step 1, if i want to regress the mean signal of CSF, white matter and gray matter separately, should I set the value of the mask "GrayWhiteCSF_mask_91_109_91.nii.gz "  from 1 to 3 (such as Gray matter as 1, white matter as 2, CSF as 3).

2) Is there a easier way to finish the steps (may not change the preprocessing order..) i did which may do not save the intermediate outputs(because it's really time-consuming). 


Thanks again.


All the best,
Meiling