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Hi Mark, Thank you very much for your time. -Yes, sometimes I use AFNI besides FSL to view images. -The Q/S-forms are 4, not zero. -Actually I have two issues: image space is fine, MNI space is coarse, so backing to MNI space lose some information. -Since I wrongly copied all the Q/S-forms from my reference image, images became stretched or shrunk. -My original image has dimentions: 256*256*128. -I ran: flirt -in image1 -ref MNI --out image2 -init identity.mat Actually I found that I should use applyxfm option also. I used this command to change the dimention and orientation of my image to MNI. May be I was wrong with saying the term "view". I meant when I look at MNI template image in FSL it shows me three views of the template, but when I look at original image, these three views are exchanged (e.g. axial of original image is replaced with coronal of MNI image) and also it is 90 degree diferent in some views (e.g. coronal of original image is vertical while MNI is horizontal). -My mask is actually a segmented image of subcortical structures. So, it is composed of 17 different integer values. Best, Siamak