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Hi, Thanks very much for the reply. I thought that the grey and white matter volumes were normalized by the "head size" through the volumetric scaling factor. So, my understanding was that given that scaling factor, I could take the ICV of the MNI152 template and back calculate the head size of the individual. And since this scaling factor is derived from the determinant of the registration of the skull image to the MNI152 template, it would yield an estimate of the intracranial volume. Am I missing something? This "method" was pieced together from a couple places, so I might be mistaken. Best, Julia ________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Stephen Smith [[log in to unmask]] Sent: Tuesday, July 17, 2012 2:05 AM To: [log in to unmask] Subject: Re: [FSL] ICV for the MNI152 template Hi - SIENAX gives you volume of grey, white, optionally "ventricular CSF", etc. but doesn't directly calculate ICV (ie including all CSF I guess) - are you sure you're comparing like with like? Cheers. On 12 Jul 2012, at 17:28, Owen, Julia wrote: Hi, I am trying to get ICVs for a group of subjects using sienax. I know that sienax will give a scaling factor between each subject and the MNI152 template, so with the volume of the MNI template, I can back calculate ICV. I found this post: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1206&L=FSL&P=R62911&1=FSL&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4, which provides a volume of 1847712 mm^3 for the MNI template. When I use this volume and compare to the ICVs obtained from SPM and FreeSurfer, I find that the ICVs from sienax are consistently 15% less than those obtained with SPM and FS. So, I can only conclude that 1847712 mm^3 is not the true volume (or there is some systematic bias, but it's easier to believe that this MNI ICV is off). Does anyone have a more accurate volume? Or any ideas about what I am doing incorrectly? Thanks in advance, Julia --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------