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Hi all, I would like to understand meaning of realignment parameters because I need to handle some data coming from a follow up study. Let say I have a patient, who came at time t_0; he has been scanned to get a *T1old,* and some datapoints on his scalp have been mapped. Those points are in voxel coordinate. The same subject came again at time t_1, he has been scanned again and new points *Pnew* have been obtained on the new scan, called *T1new*. Now, I would like to overlap new datapoints onto the T1old got at time t_0 and compare them somehow with the old datapoints. I have used *spm_realign *to get the rigid body transformation of T1new to T1old (because the images do differ from one scan to the other) Let be *V_rTnew.mat* the voxel2world matrix of the realigned *rT1new*, and *V_Told.mat* the voxel2world matrix of *Told*; I can get the transformation parameters by typing *transfparams=spm_imatrix(V_rTnew.mat/V_Told.mat)* Now, I can get the affine transformation matrix by using *spm_matrix* *affineMAT=spm_matrix(transfparams(1:6)); %it is rigid body then only 6 parameters* Eventually. I want to manually transform new datapoints, e.g., *Pnew*, in order to be overlapped onto my *Told* , becamingo finalPnew. What is the global transfotmation I have to apply?Would this procedure be working? 1) *VoxPnew* -> *V_rTnew.mat*[VoxPnew;1]=[MMPnew;1]* (to get the same coordinate in millimiters of Tnew space) 2) *MMPnew* -> *affineMAT*[MMPnew;1]=[MMtransfPnew;1]* (to transform the coordinates in the same location where they should be in the Told world space) 3) *MMtrasnfPnew* -> *inv(V_Told.mat)*[MMtrasnfPnew;1]=[finalP;1]* I am not sure for two reasons: a) I do not know whether my *affineMAT* really maps mm coords of T1new to mm coords in Told wrold space b) I do not know whether, in step 1), I should use *V_rTnew.mat *or *V_Tnew.mat* , i.e., the voxel2world matrix of the realigned new volume or the voxel2world matrix of the raw Tnew volume. I am in doubt here because I have seen that, in the header info of nifti file Tnew, there are three places where a voxel2world matrix is written: *V_Tnew.mat*, *V_Tnew.private.mat* and *V_Tnew.private.mat0*, and only the second one seems to change in rTnew volume. Can somebody please help me understanding the whole procedure? Thanks, Alessandro