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Hi, FSL experts, Thank you for all your help! Now I do follow the following steps as you tell me: 1.imcp N06 N06_orig 2. fslswapdim N06 RL PA IS N06 3.fslroi N06 N06_cropped 0 160 0 256 52 190 then chek the image using the fslview, very good! So I run the step 4 4.sienax N06_cropped.nii.gz -o N06_sienax -B "-f 0.3 -R" When this command is done, I see the report.html file and find the segment is very good. So I open the report.sienax file, just as below: SENA - Structural Image Evaluation, using Normalisation, of Atrophy part of FSL www.fmrib.ox.ac.uk/fsl running cross-sectional atrophy measurement: sienax version 2.6 sienax ---------- extract brain -------------------------------------------- ---------- register to standard space using brain and skull -------- (do not worry about histogram warnings) VSCALING 1.2515755727 ---------- mask with std mask --------------------------------------- ---------- segment tissue into types -------------------------------- ---------- convert brain volume into normalised volume -------------- tissue volume unnormalised-volume GREY 798467.69 637970.02 WHITE 703811.83 562340.65 BRAIN 1502279.52 1200310.67 So the 1502279.52 is N06's intracranial volume? Is that right? the way, Whether left Hippocampus volume which produced by FIRST tool also need VSCALING to normalise before the statistic analysis? Thank you very much!!! Best regards! your sincerely: Hankee