Hi Xenios,
Sorry to bug with the same problem. In my previous post, I do the Motion, CSF, White, gray matter regression using the following command (in bash):

# 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

it works well. However, when i add the motion correction like:
 
bis_csfwmmotioncorr --inp ${InPath}/${subject}/rfMRI_REST.nii.gz --inp2 ${TemplatePath}/GrayWhiteCSF_mask_91_109_91.nii.gz --filename ${InPath}/${subject}/rfMRI_REST_movement.mat --domotion 1 --docsfwm 1 --usemask 1 --out ${OutPath}/${subject}/rfMRI_REST_resid.nii.gz

errors exited again

Using Mask ...
Beginning vtkbisCsfWmMotionCorrection
vtk: /agrino2/src/bioimagesuite3_base_orig/InsightToolkit-3.10.0/Utilities/vxl/core/vnl/algo/vnl_svd.txx:43: vnl_svd::vnl_svd(const vnl_matrix&, double) [with T = double]: Assertion 'm_ > 0' failed.
/data/user/limeiling/SoftWare/bioimagesuite30_64/bin/bis_csfwmmotioncorr: line 24: 8395 Aborted (core dumped) ${BIS_VTK_DIR}/../../bin/vtk ${BASE}/bis_algorithm/bis_csfwmmotioncorr.tcl -- $@

my functional MRI data is 91*109*91*200, the dimension of the matlab motion file "rfMRI_REST_movement.mat"  is: 200*12 (12 motion parameters).

Actually, i didn't find the directory "/agrino2/src/bioimagesuite3_base_orig/ " ....


Meiling